Aspen/Pando, low number of variants, trouble shooting

Post date: Feb 25, 2019 4:1:51 PM

The number of variants post filtering was abysmally low. I am trying to figure out why (i.e., what went wrong).

Two observations:

A. Everything through sequence alignment looks great. See the attached report.

B. Alex uncovered a weird bug with polyploids with the HaplotypeCaller in GATK. I wonder if that is the cause of the crappy variant set.

So, I want to try variant calling again with the UnifiedGenotyper.

1. Variant calling with UG, The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56, Job ID = 6806383.

sbatch GatkUG.sh

#!/bin/sh

#SBATCH --time=336:00:00

#SBATCH --nodes=1

#SBATCH --ntasks=24

#SBATCH --account=gompert-kp

#SBATCH --partition=gompert-kp

#SBATCH --job-name=gatk-ug

#SBATCH --mail-type=FAIL

#SBATCH --mail-user=zach.gompert@usu.edu

echo ------------------------------------------------------

echo -n 'Job is running on node '; cat $SLURM_JOB_NODELIST

echo ------------------------------------------------------

echo SLURM: job identifier is $SLURM_JOBID

echo SLURM: job name is $SLURM_JOB_NAME

echo ------------------------------------------------------

module load gatk

cd /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/gbs_pando_plus/Alignments

java -Xmx480g -jar ~/bin/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /uufs/chpc.utah.edu/common/home/u6000989/data/aspen/genome/Potrs01-genome.fa -o /scratch/general/lustre/potrGatk/potr_UG.vcf -stand_call_conf 50 -ploidy 2 -nt 8 -gt_mode DISCOVERY -hets 0.001 -mbq 20 -out_mode EMIT_VARIANTS_ONLY -I aln001-B.sorted.bam -I aln001-S.sorted.bam -I aln003-B.sorted.bam -I aln003-S-rep.sorted.bam -I aln003-S-Rp.sorted.bam -I aln003-S.sorted.bam -I aln005-B.sorted.bam -I aln005-S.sorted.bam -I aln007-B.sorted.bam -I aln007-S.sorted.bam -I aln009-B.sorted.bam -I aln009-S.sorted.bam -I aln011-B.sorted.bam -I aln011-S.sorted.bam -I aln013-B.sorted.bam -I aln013-S.sorted.bam -I aln015-B.sorted.bam -I aln015-S.sorted.bam -I aln017-B.sorted.bam -I aln017-S.sorted.bam -I aln019-B.sorted.bam -I aln019-S.sorted.bam -I aln021-B.sorted.bam -I aln021-S.sorted.bam -I aln022-S.sorted.bam -I aln023-B.sorted.bam -I aln023-S.sorted.bam -I aln025-B.sorted.bam -I aln025-S.sorted.bam -I aln027-B.sorted.bam -I aln029-B.sorted.bam -I aln031-B.sorted.bam -I aln031-S.sorted.bam -I aln033-B.sorted.bam -I aln033-S.sorted.bam -I aln035-B.sorted.bam -I aln035-S.sorted.bam -I aln037-B-rep.sorted.bam -I aln037-B-Rp.sorted.bam -I aln037-B.sorted.bam -I aln037-S.sorted.bam -I aln039-B.sorted.bam -I aln039-S.sorted.bam -I aln041-B.sorted.bam -I aln041-S.sorted.bam -I aln043-B.sorted.bam -I aln043-S.sorted.bam -I aln045-S.sorted.bam -I aln047-B2.sorted.bam -I aln047-B.sorted.bam -I aln047-S.sorted.bam -I aln049-B.sorted.bam -I aln049-S.sorted.bam -I aln051-B.sorted.bam -I aln051-S.sorted.bam -I aln053-B.sorted.bam -I aln053-S.sorted.bam -I aln055-B.sorted.bam -I aln055-S-rep.sorted.bam -I aln055-S-Rp.sorted.bam -I aln055-S.sorted.bam -I aln059-S.sorted.bam -I aln061-B.sorted.bam -I aln061-S.sorted.bam -I aln063-S.sorted.bam -I aln065-B.sorted.bam -I aln065-S.sorted.bam -I aln067-B.sorted.bam -I aln067-S.sorted.bam -I aln069-B.sorted.bam -I aln069-S.sorted.bam -I aln071-B.sorted.bam -I aln073-B.sorted.bam 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alnAZN-1625.sorted.bam -I alnAZN-1626.sorted.bam -I alnAZN-1627.sorted.bam -I alnAZN-1628.sorted.bam -I alnAZN-1629-Rp.sorted.bam -I alnAZN-1629.sorted.bam -I alnAZN-1630.sorted.bam -I alnAZN-1631.sorted.bam -I alnAZN-1632.sorted.bam -I alnAZN-1633.sorted.bam -I alnAZN-1634.sorted.bam -I alnAZN-1635.sorted.bam -I alnAZN-1636.sorted.bam -I alnAZN-1637.sorted.bam -I alnAZN-1638-RpA130.sorted.bam -I alnAZN-1638.sorted.bam -I alnAZN-1639.sorted.bam -I alnAZN-1640.sorted.bam -I alnAZN-1641.sorted.bam -I alnAZN-1642.sorted.bam -I alnAZN-1643.sorted.bam -I alnAZN-1644.sorted.bam -I alnAZN-1645.sorted.bam -I alnAZN-1646.sorted.bam -I alnAZN-1647.sorted.bam -I alnAZN-1648-Rp.sorted.bam -I alnAZN-1648.sorted.bam -I alnAZN-1649.sorted.bam -I alnAZN-1650.sorted.bam -I alnAZW-1601.sorted.bam -I alnAZW-1602.sorted.bam -I alnAZW-1603.sorted.bam -I alnAZW-1604.sorted.bam -I alnAZW-1605.sorted.bam -I alnAZW-1606.sorted.bam -I alnAZW-1607.sorted.bam -I alnAZW-1608.sorted.bam -I alnAZW-1609.sorted.bam -I alnAZW-1610.sorted.bam -I alnAZW-1611.sorted.bam -I alnAZW-1612.sorted.bam -I alnAZW-1613.sorted.bam -I alnAZW-1614.sorted.bam -I alnAZW-1615.sorted.bam -I alnAZW-1616.sorted.bam -I alnAZW-1617.sorted.bam -I alnAZW-1618.sorted.bam -I alnAZW-1619.sorted.bam -I alnAZW-1620.sorted.bam -I alnAZW-1621.sorted.bam -I alnAZW-1622.sorted.bam -I alnAZW-1623.sorted.bam -I alnAZW-1624.sorted.bam -I alnAZW-1625.sorted.bam -I alnAZW-1626.sorted.bam -I alnAZW-1627.sorted.bam -I alnAZW-1628.sorted.bam -I alnAZW-1629.sorted.bam -I alnAZW-1630.sorted.bam -I alnAZW-1631.sorted.bam -I alnAZW-1632.sorted.bam -I alnAZW-1633.sorted.bam -I alnAZW-1634.sorted.bam -I alnAZW-1635.sorted.bam -I alnAZW-1636.sorted.bam -I alnAZW-1637-RpA130.sorted.bam -I alnAZW-1637.sorted.bam -I alnAZW-1638.sorted.bam -I alnAZW-1639.sorted.bam -I alnAZW-1640.sorted.bam -I alnAZW-1641.sorted.bam -I alnAZW-1642.sorted.bam -I alnAZW-1643.sorted.bam -I alnAZW-1644.sorted.bam -I alnAZW-1645.sorted.bam -I alnAZW-1646.sorted.bam -I alnAZW-1647.sorted.bam -I alnAZW-1648.sorted.bam -I alnAZW-1649.sorted.bam -I alnAZW-1650.sorted.bam -I alnBCG-1601.sorted.bam -I alnBCG-1602.sorted.bam -I alnBCG-1603.sorted.bam -I alnBM-2.sorted.bam -I alnBMR-0193.sorted.bam -I alnBR-1.sorted.bam -I alnBR-2.sorted.bam -I alnBR-4.sorted.bam -I alnBR-5.sorted.bam -I alnBSF-3458B.sorted.bam -I alnCAM-1601.sorted.bam -I alnCAM-1602.sorted.bam -I alnCAM-1603.sorted.bam -I alnCAM-1604.sorted.bam -I alnCAM-1605-RpA149.sorted.bam -I alnCAM-1605.sorted.bam -I alnCAM-1606.sorted.bam -I alnCAM-1607.sorted.bam -I alnCAM-1608.sorted.bam -I alnCAM-1609-Rp.sorted.bam -I alnCAM-1609.sorted.bam -I alnCAM-1610.sorted.bam -I alnCAM-1611.sorted.bam -I alnCAM-1612.sorted.bam -I alnCAM-1613.sorted.bam -I alnCAM-1614.sorted.bam -I alnCAM-1615.sorted.bam -I alnCAM-1616.sorted.bam -I alnCAM-1617.sorted.bam -I alnCAM-1618.sorted.bam -I alnCAM-1619.sorted.bam -I alnCAM-1620-Rp.sorted.bam -I alnCAM-1620.sorted.bam -I alnCAM-1621.sorted.bam -I alnCAM-1622.sorted.bam -I alnCAM-1623.sorted.bam -I alnCAM-1624.sorted.bam -I alnCAM-1625.sorted.bam -I alnCAM-1626.sorted.bam -I alnCAM-1627.sorted.bam -I alnCAM-1628.sorted.bam -I alnCAM-1629.sorted.bam -I alnCAM-1630.sorted.bam -I alnCAM-1631.sorted.bam -I alnCAM-1632.sorted.bam -I alnCAM-1633.sorted.bam -I alnCAM-1634.sorted.bam -I alnCAM-1635-Rp.sorted.bam -I alnCAM-1635.sorted.bam -I alnCAM-1636.sorted.bam -I alnCAM-1637.sorted.bam -I alnCAM-1638.sorted.bam -I alnCAM-1639.sorted.bam -I alnCAM-1640.sorted.bam -I alnCAM-1641.sorted.bam -I alnCAM-1642.sorted.bam -I alnCAM-1643.sorted.bam -I alnCAM-1644.sorted.bam -I alnCAM-1645.sorted.bam -I alnCAM-1646.sorted.bam -I alnCAM-1647.sorted.bam -I alnCAM-1648.sorted.bam -I alnCAM-1649.sorted.bam -I alnCAM-1650.sorted.bam -I alnCAM-1651.sorted.bam -I alnCAM-1652.sorted.bam -I alnCAR-1601.sorted.bam -I alnCAR-1602.sorted.bam -I alnCAR-1603.sorted.bam -I alnCAR-1604.sorted.bam -I alnCAR-1605.sorted.bam -I alnCAR-1606.sorted.bam -I alnCAR-1607.sorted.bam -I alnCAR-1608.sorted.bam -I alnCAR-1609.sorted.bam -I alnCAR-1610.sorted.bam -I alnCAR-1611.sorted.bam -I alnCAR-1612.sorted.bam -I alnCAR-1613.sorted.bam -I alnCAR-1614.sorted.bam -I alnCAR-1615.sorted.bam -I alnCAR-1616.sorted.bam -I alnCAR-1617.sorted.bam -I alnCAR-1618.sorted.bam -I alnCAR-1619.sorted.bam -I alnCAR-1620.sorted.bam -I alnCAR-1621.sorted.bam -I alnCAR-1622.sorted.bam -I alnCAR-1623.sorted.bam -I alnCAR-1624.sorted.bam -I alnCAR-1625-Rp.sorted.bam -I alnCAR-1625.sorted.bam -I alnCAR-1626.sorted.bam -I alnCAR-1627.sorted.bam -I alnCAR-1628.sorted.bam -I alnCAR-1629.sorted.bam -I alnCAR-1630.sorted.bam -I alnCAR-1631.sorted.bam -I alnCAR-1632.sorted.bam -I alnCAR-1633.sorted.bam -I alnCAR-1634.sorted.bam -I alnCAR-1635.sorted.bam -I alnCAR-1636.sorted.bam -I alnCAR-1637.sorted.bam -I alnCAR-1638.sorted.bam -I alnCAR-1639-Rp.sorted.bam -I alnCAR-1639.sorted.bam -I alnCAR-1640.sorted.bam -I alnCAR-1641.sorted.bam -I alnCAR-1642.sorted.bam -I alnCAR-1643.sorted.bam -I alnCAR-1644.sorted.bam -I alnCAR-1645.sorted.bam -I alnCAR-1646.sorted.bam -I alnCAR-1647-Rp.sorted.bam -I alnCAR-1647.sorted.bam -I alnCAR-1648.sorted.bam -I alnCAR-1649-Rp.sorted.bam -I alnCAR-1649.sorted.bam -I alnCAR-1650.sorted.bam -I alnCOC-1601.sorted.bam -I alnCOC-1602.sorted.bam -I alnCOC-1603.sorted.bam -I alnCOC-1604.sorted.bam -I alnCOC-1605.sorted.bam -I alnCOC-1606-Rp.sorted.bam -I alnCOC-1606.sorted.bam -I alnCOC-1607.sorted.bam -I alnCOC-1608.sorted.bam -I alnCOC-1609-Rp.sorted.bam -I alnCOC-1609.sorted.bam -I alnCOC-1610.sorted.bam -I alnCOC-1611.sorted.bam -I alnCOC-1612.sorted.bam -I alnCOC-1613.sorted.bam -I alnCOC-1614.sorted.bam -I alnCOC-1615.sorted.bam -I alnCOC-1616.sorted.bam -I alnCOC-1617.sorted.bam -I alnCOC-1618.sorted.bam -I alnCOC-1619.sorted.bam -I alnCOC-1620.sorted.bam -I alnCOC-1621.sorted.bam -I alnCOC-1622.sorted.bam -I alnCOC-1623.sorted.bam -I alnCOC-1624.sorted.bam -I alnCOC-1625.sorted.bam -I alnCOC-1626.sorted.bam -I alnCOC-1627.sorted.bam -I alnCOC-1628-Rp.sorted.bam -I alnCOC-1628.sorted.bam -I alnCOC-1629-Rp.sorted.bam -I alnCOC-1629.sorted.bam -I alnCOC-1630.sorted.bam -I alnCOC-1631.sorted.bam -I alnCOC-1632.sorted.bam -I alnCOC-1633.sorted.bam -I alnCOC-1634.sorted.bam -I alnCOC-1635.sorted.bam -I alnCOC-1636.sorted.bam -I alnCOC-1637.sorted.bam -I alnCOC-1638.sorted.bam -I alnCOC-1639.sorted.bam -I alnCOC-1640.sorted.bam -I alnCOC-1641.sorted.bam -I alnCOC-1642.sorted.bam -I alnCOC-1643.sorted.bam -I alnCOC-1644.sorted.bam -I alnCOC-1645.sorted.bam -I alnCOC-1646.sorted.bam -I alnCOC-1647.sorted.bam -I alnCOC-1648.sorted.bam -I alnCOC-1649.sorted.bam -I alnCOC-1650.sorted.bam -I alnCOD-1601.sorted.bam -I alnCOD-1602.sorted.bam -I alnCOD-1603.sorted.bam -I alnCOD-1604-RpA131.sorted.bam -I alnCOD-1604.sorted.bam -I alnCOD-1605.sorted.bam -I alnCOD-1606.sorted.bam -I alnCOD-1607.sorted.bam -I alnCOD-1608.sorted.bam -I alnCOD-1609.sorted.bam -I alnCOD-1610.sorted.bam -I alnCOD-1611.sorted.bam -I alnCOD-1612.sorted.bam -I alnCOD-1613.sorted.bam -I alnCOD-1614.sorted.bam -I alnCOD-1615.sorted.bam -I alnCOD-1616.sorted.bam -I alnCOD-1617.sorted.bam -I alnCOD-1618.sorted.bam -I alnCOD-1619.sorted.bam -I alnCOD-1620.sorted.bam -I alnCOD-1621.sorted.bam -I alnCOH-1601.sorted.bam -I alnCOH-1602.sorted.bam -I alnCOH-1603.sorted.bam -I alnCOH-1604.sorted.bam -I alnCOH-1605.sorted.bam -I alnCOH-1606.sorted.bam -I alnCOH-1607.sorted.bam -I alnCOH-1608.sorted.bam -I alnCOH-1609.sorted.bam -I alnCOH-1610.sorted.bam -I alnCOH-1611.sorted.bam -I alnCOH-1612.sorted.bam -I alnCOH-1613.sorted.bam -I alnCOH-1614.sorted.bam -I alnCOH-1615.sorted.bam -I alnCOH-1616.sorted.bam -I alnCOH-1617.sorted.bam -I alnCOH-1618-RpA131.sorted.bam -I alnCOH-1618.sorted.bam -I alnCOH-1619.sorted.bam -I alnCOH-1620.sorted.bam -I alnCOH-1621.sorted.bam -I alnCOH-1622.sorted.bam -I alnCOH-1623-Rp.sorted.bam -I alnCOH-1623.sorted.bam -I alnCOH-1624.sorted.bam -I alnCOH-1625.sorted.bam -I alnCOH-1626.sorted.bam -I alnCOH-1627.sorted.bam -I alnCOH-1628.sorted.bam -I alnCOH-1629.sorted.bam -I alnCOH-1630.sorted.bam -I alnCOH-1631.sorted.bam -I alnCOH-1632.sorted.bam -I alnCOH-1633.sorted.bam -I alnCOH-1634.sorted.bam -I alnCOH-1635.sorted.bam -I alnCOH-1636-Rp.sorted.bam -I alnCOH-1636.sorted.bam -I alnCOH-1637.sorted.bam -I alnCOH-1638.sorted.bam -I alnCOH-1639.sorted.bam -I alnCOH-1640.sorted.bam -I alnCOH-1641.sorted.bam -I alnCOH-1642.sorted.bam -I alnCOH-1643.sorted.bam -I alnCOH-1644.sorted.bam -I alnCOH-1645.sorted.bam -I alnCOH-1646.sorted.bam -I alnCOH-1647.sorted.bam -I alnCOH-1648.sorted.bam -I alnCOH-1649.sorted.bam -I alnCOH-1650.sorted.bam -I alnCOH-1651.sorted.bam -I alnCOH-16CW.sorted.bam -I alnCOM-1601.sorted.bam -I alnCOM-1602.sorted.bam -I alnCOM-1603.sorted.bam -I alnCOM-1604.sorted.bam -I alnCOM-1605.sorted.bam -I alnCOM-1606.sorted.bam -I alnCOM-1607.sorted.bam -I alnCOM-1608.sorted.bam -I alnCOM-1609.sorted.bam -I alnCOM-1610.sorted.bam -I alnCOM-1611.sorted.bam -I alnCOM-1612.sorted.bam -I alnCOM-1613.sorted.bam -I alnCOM-1614.sorted.bam -I alnCOM-1615.sorted.bam -I alnCOM-1616.sorted.bam -I alnCOM-1617.sorted.bam -I alnCOM-1618.sorted.bam -I alnCOM-1619.sorted.bam -I alnCOM-1620.sorted.bam -I alnCOM-1621.sorted.bam -I alnCOM-1622.sorted.bam -I alnCOM-1623.sorted.bam -I alnCOM-1624.sorted.bam -I alnCOM-1625.sorted.bam -I alnCOM-1626.sorted.bam -I alnCOM-1627.sorted.bam -I alnCOM-1628.sorted.bam -I alnCOM-1629.sorted.bam -I alnCOM-1630.sorted.bam -I alnCOM-1631.sorted.bam -I alnCOM-1632-RpA132.sorted.bam -I alnCOM-1632.sorted.bam -I alnCOM-1633.sorted.bam -I alnCOM-1634.sorted.bam -I alnCOM-1635.sorted.bam -I alnCOM-1636.sorted.bam -I alnCOM-1637.sorted.bam -I alnCOM-1638.sorted.bam -I alnCOM-1639.sorted.bam -I alnCOM-1640-RpA132.sorted.bam -I alnCOM-1640.sorted.bam -I alnCOM-1641.sorted.bam -I alnCOM-1642.sorted.bam -I alnCOM-1643.sorted.bam -I alnCOM-1644.sorted.bam -I alnCOM-1645.sorted.bam -I alnCOM-1646.sorted.bam -I alnCOM-1647-Rp.sorted.bam -I alnCOM-1647.sorted.bam -I alnCOM-1648-Rp.sorted.bam -I alnCOM-1648.sorted.bam -I alnCOM-1649.sorted.bam -I alnCOM-1650.sorted.bam -I alnCOP-1601.sorted.bam -I alnCOP-1602.sorted.bam -I alnCOP-1603.sorted.bam -I alnCOP-1604.sorted.bam -I alnCOP-1605.sorted.bam -I alnCOP-1606.sorted.bam -I alnCOP-1607.sorted.bam -I alnCOP-1608.sorted.bam -I alnCOP-1609.sorted.bam -I alnCOP-1610.sorted.bam -I alnCOP-1611.sorted.bam -I alnCOP-1612.sorted.bam -I alnCOP-1613.sorted.bam -I alnCOP-1614.sorted.bam -I alnCOP-1615.sorted.bam -I alnCOP-1616.sorted.bam -I alnCOP-1617.sorted.bam -I alnCOP-1618.sorted.bam -I alnCOP-1619.sorted.bam -I alnCOP-1620.sorted.bam -I alnCOP-1621.sorted.bam -I alnCOP-1622.sorted.bam -I alnCOP-1623.sorted.bam -I alnCOP-1624-RpA133.sorted.bam -I alnCOP-1624.sorted.bam -I alnCOP-1625.sorted.bam -I alnCOP-1626.sorted.bam -I alnCOP-1627.sorted.bam -I alnCOP-1628.sorted.bam -I alnCOP-1629.sorted.bam -I alnCOP-1630.sorted.bam -I alnCOP-1631.sorted.bam -I alnCOP-1632.sorted.bam -I alnCOP-1633.sorted.bam -I alnCOP-1634.sorted.bam -I alnCOP-1635.sorted.bam -I alnCOP-1636.sorted.bam -I alnCOP-1637.sorted.bam -I alnCOP-1638.sorted.bam -I alnCOP-1639.sorted.bam -I alnCOP-1640.sorted.bam -I alnCOP-1641.sorted.bam -I alnCOP-1642.sorted.bam -I alnCOP-1643.sorted.bam -I alnCOP-1644.sorted.bam -I alnCOP-1645.sorted.bam -I alnCOP-1646.sorted.bam -I alnCOP-1647.sorted.bam -I alnCOP-1648.sorted.bam -I alnCOP-1649.sorted.bam -I alnCOP-1650.sorted.bam -I alnCOS-1601.sorted.bam -I alnCOS-1602.sorted.bam -I alnCOS-1603.sorted.bam -I alnCOS-1604.sorted.bam -I alnCOS-1605.sorted.bam -I alnCOS-1606.sorted.bam -I alnCOS-1607.sorted.bam -I alnCOS-1608.sorted.bam -I alnCOS-1609.sorted.bam -I alnCOS-1610-RpA133.sorted.bam -I alnCOS-1610.sorted.bam -I alnCOS-1611.sorted.bam -I alnCOS-1612.sorted.bam -I alnCOS-1613.sorted.bam -I alnCOS-1614.sorted.bam -I alnCOS-1615-Rp.sorted.bam -I alnCOS-1615.sorted.bam -I alnCOS-1616.sorted.bam -I alnCOS-1617.sorted.bam -I alnCOS-1618.sorted.bam -I alnCOS-1619.sorted.bam -I alnCOS-1620.sorted.bam -I alnCOS-1621.sorted.bam -I alnCOS-1622.sorted.bam -I alnCOS-1623.sorted.bam -I alnCOS-1624.sorted.bam -I alnCOS-1625.sorted.bam -I alnCOS-1626.sorted.bam -I alnCOS-1627.sorted.bam -I alnCOS-1628.sorted.bam -I alnCOS-1629.sorted.bam -I alnCOS-1630.sorted.bam -I alnCOS-1631.sorted.bam -I alnCOS-1632.sorted.bam -I alnCOS-1633.sorted.bam -I alnCOS-1634.sorted.bam -I alnCOS-1635.sorted.bam -I alnCOS-1636.sorted.bam -I alnCOS-1637.sorted.bam -I alnCOS-1638-Rp.sorted.bam -I alnCOS-1638.sorted.bam -I alnCOS-1639.sorted.bam -I alnCOS-1640.sorted.bam -I alnCOS-1641.sorted.bam -I alnCOS-1642.sorted.bam -I alnCOS-1643.sorted.bam -I alnCOS-1644.sorted.bam -I alnCOS-1645.sorted.bam -I alnCOS-1646.sorted.bam -I alnCOS-1647.sorted.bam -I alnCOS-1648.sorted.bam -I alnCOS-1649.sorted.bam -I alnCOS-1650.sorted.bam -I alnCOS-1651.sorted.bam -I alnCOS-16CW.sorted.bam -I alnCOT-1601-Rp.sorted.bam -I alnCOT-1601.sorted.bam -I alnCOT-1602.sorted.bam -I alnCOT-1603.sorted.bam -I alnCOT-1604.sorted.bam -I alnCOT-1605.sorted.bam -I alnCOT-1606.sorted.bam -I alnCOT-1607.sorted.bam -I alnCOT-1608.sorted.bam -I alnCOT-1609.sorted.bam -I alnCOT-1610.sorted.bam -I alnCOT-1611.sorted.bam -I alnCOT-1612.sorted.bam -I alnCOT-1613.sorted.bam -I alnCOT-1614.sorted.bam -I alnCOT-1615-Rp.sorted.bam -I alnCOT-1615.sorted.bam -I alnCOT-1616.sorted.bam -I alnCOT-1617.sorted.bam -I alnCOT-1618.sorted.bam -I alnCOT-1619.sorted.bam -I alnCOT-1620.sorted.bam -I alnCOT-1621.sorted.bam -I alnCOT-1622.sorted.bam -I alnCOT-1623.sorted.bam -I alnCOT-1624.sorted.bam -I alnCOT-1625.sorted.bam -I alnCOT-1626.sorted.bam -I alnCOT-1627.sorted.bam -I alnCOT-1628.sorted.bam -I alnCOT-1629.sorted.bam -I alnCOT-1630.sorted.bam -I alnCOT-1631.sorted.bam -I alnCOT-1632.sorted.bam -I alnCOT-1633.sorted.bam -I alnCOT-1634.sorted.bam -I alnCOT-1635-Rp.sorted.bam -I alnCOT-1635.sorted.bam -I alnCOT-1636.sorted.bam -I alnCOT-1637.sorted.bam -I alnCOT-1638.sorted.bam -I alnCOT-1639.sorted.bam -I alnCOT-1640-RpA134.sorted.bam -I alnCOT-1640.sorted.bam -I alnCOT-1641.sorted.bam -I alnCOT-1642.sorted.bam -I alnCOT-1643.sorted.bam -I alnCOT-1644.sorted.bam -I alnCOT-1645.sorted.bam -I alnCOT-1646.sorted.bam -I alnCOT-1647-RpA134.sorted.bam -I alnCOT-1647.sorted.bam -I alnCOT-1648.sorted.bam -I alnCOT-1649.sorted.bam -I alnCOT-1650.sorted.bam -I alnCOU-1601.sorted.bam -I alnCOU-1602.sorted.bam -I alnCOU-1603.sorted.bam -I alnCOU-1604.sorted.bam -I alnCOU-1605-Rp.sorted.bam -I alnCOU-1605.sorted.bam -I alnCOU-1606.sorted.bam -I alnCOU-1607.sorted.bam -I alnCOU-1608.sorted.bam -I alnCOU-1609.sorted.bam -I alnCOU-1610.sorted.bam -I alnCOU-1611.sorted.bam -I alnCOU-1612.sorted.bam -I alnCOU-1613-RpA139.sorted.bam -I alnCOU-1613.sorted.bam -I alnCOU-1614.sorted.bam -I alnCOU-1615.sorted.bam -I alnCOU-1616.sorted.bam -I alnCOU-1617.sorted.bam -I alnCOU-1618.sorted.bam -I alnCOU-1619.sorted.bam -I alnCOU-1620.sorted.bam -I alnCOU-1621.sorted.bam -I alnCOU-1622.sorted.bam -I alnCOU-1623.sorted.bam -I alnCOU-1624.sorted.bam -I alnCOU-1625.sorted.bam -I alnCOU-1626.sorted.bam -I alnCOU-1627.sorted.bam -I alnCOU-1628.sorted.bam -I alnCOU-1629.sorted.bam -I alnCOU-1630.sorted.bam -I alnCOU-1631.sorted.bam -I alnCOU-1632.sorted.bam -I alnCOU-1633.sorted.bam -I alnCOU-1634.sorted.bam -I alnCOU-1635.sorted.bam -I alnCOU-1636.sorted.bam -I alnCOU-1637.sorted.bam -I alnCOU-1638.sorted.bam -I alnCOU-1639.sorted.bam -I alnCOU-1640.sorted.bam -I alnCOU-1641.sorted.bam -I alnCOU-1642.sorted.bam -I alnCOU-1643.sorted.bam -I alnCOU-1644.sorted.bam -I alnCOU-1645.sorted.bam -I alnCOU-1646.sorted.bam -I alnCOU-1647.sorted.bam -I alnCOU-1648.sorted.bam -I alnCOU-1649.sorted.bam -I alnCOU-1650.sorted.bam -I alnCOV-1601.sorted.bam -I alnCOV-1602.sorted.bam -I alnCOV-1603.sorted.bam -I alnCOV-1604.sorted.bam -I alnCOV-1605.sorted.bam -I alnCOV-1606.sorted.bam -I alnCOV-1607.sorted.bam -I alnCOV-1608.sorted.bam -I alnCOV-1609.sorted.bam -I alnCOV-1610.sorted.bam -I alnCOV-1611.sorted.bam -I alnCOV-1612.sorted.bam -I alnCOV-1613.sorted.bam -I alnCOV-1614.sorted.bam -I alnCOV-1615-Rp.sorted.bam -I alnCOV-1615.sorted.bam -I alnCOV-1616.sorted.bam -I alnCOV-1617.sorted.bam -I alnCOV-1618.sorted.bam -I alnCOV-1619-A135.sorted.bam -I alnCOV-1619.sorted.bam -I alnCOV-1620.sorted.bam -I alnCOV-1621.sorted.bam -I alnCOV-1622.sorted.bam -I alnCOV-1623.sorted.bam -I alnCOV-1624.sorted.bam -I alnCOV-1625.sorted.bam -I alnCOV-1626.sorted.bam -I alnCOV-1627.sorted.bam -I alnCOV-1628.sorted.bam -I alnCOV-1629.sorted.bam -I alnCOV-1630.sorted.bam -I alnCOV-1631.sorted.bam -I alnCOV-1632.sorted.bam -I alnCOV-1633.sorted.bam -I alnCOV-1634.sorted.bam -I alnCOV-1635.sorted.bam -I alnCOV-1636.sorted.bam -I alnCOV-1637.sorted.bam -I alnCOV-1638.sorted.bam -I alnCOV-1639.sorted.bam -I alnCOV-1640.sorted.bam -I alnCOV-1641.sorted.bam -I alnCOV-1642.sorted.bam -I alnCOV-1643.sorted.bam -I alnCOV-1644.sorted.bam -I alnCOV-1645.sorted.bam -I alnCOV-1646.sorted.bam -I alnCOV-1647.sorted.bam -I alnCOV-1648.sorted.bam -I alnCOV-1649.sorted.bam -I alnCOV-1650-Rp.sorted.bam -I alnCOV-1650.sorted.bam -I alnEAT-2.sorted.bam -I alnFBR-0130.sorted.bam -I alnFBR-2.sorted.bam -I alnFBR-3655.sorted.bam -I alnGCB-1.sorted.bam -I alnGCB-2.sorted.bam -I alnGCB-3.sorted.bam -I alnH2O.sorted.bam -I alnIDA-1601.sorted.bam -I alnIDA-1602.sorted.bam -I alnIDA-1603.sorted.bam -I alnIDA-1604.sorted.bam -I alnIDA-1605-RpA135.sorted.bam -I alnIDA-1605.sorted.bam -I alnIDA-1606.sorted.bam -I alnIDA-1608.sorted.bam -I alnIDA-1609.sorted.bam -I alnIDA-1610.sorted.bam -I alnIDA-1611.sorted.bam -I alnIDA-1612.sorted.bam -I alnIDA-1613.sorted.bam -I alnIDA-1614.sorted.bam -I alnIDA-1615.sorted.bam -I alnIDA-1616.sorted.bam -I alnIDA-1617.sorted.bam -I alnIDA-1618.sorted.bam -I alnIDA-1619.sorted.bam -I alnIDA-1620.sorted.bam -I alnIDA-1621.sorted.bam -I alnIDA-1622.sorted.bam -I alnIDA-1623.sorted.bam -I alnIDA-1624.sorted.bam -I alnIDA-1625.sorted.bam -I alnIDA-1626.sorted.bam -I alnIDA-1627.sorted.bam -I alnIDA-1628.sorted.bam -I alnIDA-1629.sorted.bam -I alnIDA-1630.sorted.bam -I alnIDA-1631.sorted.bam -I alnIDB-1601.sorted.bam -I alnIDB-1602.sorted.bam -I alnIDI-1601.sorted.bam -I alnIDI-1602.sorted.bam -I alnIDI-1603.sorted.bam -I alnIDI-1604.sorted.bam -I alnIDI-1605.sorted.bam -I alnIDI-1606-Rp.sorted.bam -I alnIDI-1606.sorted.bam -I alnIDI-1607.sorted.bam -I alnIDI-1608.sorted.bam -I alnIDI-1609.sorted.bam -I alnIDI-1610.sorted.bam -I alnIDI-1611.sorted.bam -I alnIDI-1612.sorted.bam -I alnIDI-1613.sorted.bam -I alnIDI-1614.sorted.bam -I alnIDI-1615.sorted.bam -I alnIDI-1616.sorted.bam -I alnIDI-1617-Rp.sorted.bam -I alnIDI-1617.sorted.bam -I alnIDI-1618.sorted.bam -I alnIDI-1619.sorted.bam -I alnIDI-1620.sorted.bam -I alnIDI-1621.sorted.bam -I alnIDI-1622.sorted.bam -I alnIDI-1623-Rp.sorted.bam -I alnIDI-1623.sorted.bam -I alnIDI-1624.sorted.bam -I alnIDI-1625.sorted.bam -I alnIDI-1626-RpA137.sorted.bam -I alnIDI-1626.sorted.bam -I alnIDI-1627.sorted.bam -I alnIDI-1628.sorted.bam -I alnIDI-1629.sorted.bam -I alnIDI-1630.sorted.bam -I alnIDI-1631.sorted.bam -I alnIDI-1632.sorted.bam -I alnIDI-1633.sorted.bam -I alnIDI-1634.sorted.bam -I alnIDI-1635.sorted.bam -I alnIDI-1636.sorted.bam -I alnIDI-1637.sorted.bam -I alnIDI-1638.sorted.bam -I alnIDI-1639.sorted.bam -I alnIDI-1640.sorted.bam -I alnIDI-1641.sorted.bam -I alnIDI-1642.sorted.bam -I alnIDI-1643.sorted.bam -I alnIDI-1644.sorted.bam -I alnIDI-1645.sorted.bam -I alnIDI-1646.sorted.bam -I alnIDI-1647.sorted.bam -I alnIDI-1648.sorted.bam -I alnIDI-1649.sorted.bam -I alnIDI-1650.sorted.bam -I alnIDS-1601.sorted.bam -I alnIDS-1602.sorted.bam -I alnIDS-1603.sorted.bam -I alnIDS-1604.sorted.bam -I alnIDS-1605.sorted.bam -I alnIDS-1606.sorted.bam -I alnIDS-1607.sorted.bam -I alnIDS-1608.sorted.bam -I alnIDS-1609.sorted.bam -I alnIDS-1610.sorted.bam -I alnIDS-1611.sorted.bam -I alnIDS-1612.sorted.bam -I alnIDS-1613.sorted.bam -I alnIDS-1614.sorted.bam -I alnIDS-1615.sorted.bam -I alnIDS-1616-RpA136.sorted.bam -I alnIDS-1616.sorted.bam -I alnIDS-1617.sorted.bam -I alnIDS-1618.sorted.bam -I alnIDS-1619.sorted.bam -I alnIDS-1620.sorted.bam -I alnIDS-1621.sorted.bam -I alnIDS-1622-Rp.sorted.bam -I alnIDS-1622.sorted.bam -I alnIDS-1623.sorted.bam -I alnIDS-1624.sorted.bam -I alnIDS-1625.sorted.bam -I alnIDS-1626.sorted.bam -I alnIDS-1627.sorted.bam -I alnIDS-1628.sorted.bam -I alnIDS-1629.sorted.bam -I alnIDS-1630.sorted.bam -I alnIDS-1631.sorted.bam -I alnIDS-1632.sorted.bam -I alnIDS-1633.sorted.bam -I alnIDS-1634.sorted.bam -I alnIDS-1635.sorted.bam -I alnIDS-1636.sorted.bam -I alnIDS-1637.sorted.bam -I alnIDS-1638.sorted.bam -I alnIDS-1639.sorted.bam -I alnIDS-1640.sorted.bam -I alnIDS-1641.sorted.bam -I alnIDS-1642.sorted.bam -I alnIDT-1601.sorted.bam -I alnIDT-1602.sorted.bam -I alnIDT-1603.sorted.bam -I alnIDT-1604.sorted.bam -I alnIDT-1605.sorted.bam -I alnIDT-1606.sorted.bam -I alnIDT-1607.sorted.bam -I alnIDT-1608.sorted.bam -I alnIDT-1609.sorted.bam -I alnIDT-1610.sorted.bam -I alnIDT-1611.sorted.bam -I alnIDT-1612.sorted.bam -I alnIDT-1613.sorted.bam -I alnIDT-1614-RpA137.sorted.bam -I alnIDT-1614.sorted.bam -I alnIDT-1615.sorted.bam -I alnIDT-1616.sorted.bam -I alnIDT-1617.sorted.bam -I alnIDT-1618.sorted.bam -I alnIDT-1619.sorted.bam -I alnIDT-1620.sorted.bam -I alnIDT-1621.sorted.bam -I alnIDT-1622.sorted.bam -I alnIDT-1623.sorted.bam -I alnIDT-1624.sorted.bam -I alnIDT-1625.sorted.bam -I alnIDT-1626.sorted.bam -I alnIDT-1627.sorted.bam -I alnIDT-1628.sorted.bam -I alnIDT-1629.sorted.bam -I alnIDT-1630.sorted.bam -I alnIDT-1631.sorted.bam -I alnIDT-1632.sorted.bam -I alnIDT-1633.sorted.bam -I alnIDT-1634.sorted.bam -I alnIDT-1635.sorted.bam -I alnIDT-1636.sorted.bam -I alnIDT-1637.sorted.bam -I alnIDT-1638.sorted.bam -I alnIDT-1639.sorted.bam -I alnIDT-1640.sorted.bam -I alnIDT-1641.sorted.bam -I alnIDT-1642.sorted.bam -I alnIDT-1643.sorted.bam -I alnIDT-1644.sorted.bam -I alnIDT-1645-Rp.sorted.bam -I alnIDT-1645.sorted.bam -I alnIDT-1646.sorted.bam -I alnIDT-1647.sorted.bam -I alnIDT-1648.sorted.bam -I alnIDT-1649.sorted.bam -I alnIDT-1650.sorted.bam -I alnIMC-0118.sorted.bam -I alnIMC-0138.sorted.bam -I alnLRK-1.sorted.bam -I alnMCR-0146.sorted.bam -I alnNeg-A000a.sorted.bam -I alnNeg-A000b.sorted.bam -I alnNeg-A128.sorted.bam -I alnNeg-A129.sorted.bam -I alnNeg-A130.sorted.bam -I alnNeg-A131.sorted.bam -I alnNeg-A132.sorted.bam -I alnNeg-A133.sorted.bam -I alnNeg-A134.sorted.bam -I alnNeg-A135.sorted.bam -I alnNeg-A136.sorted.bam -I alnNeg-A137.sorted.bam -I alnNeg-A138.sorted.bam -I alnNeg-A139.sorted.bam -I alnNeg-A140.sorted.bam -I alnNeg-A141.sorted.bam -I alnNeg-A142.sorted.bam -I alnNeg-A143.sorted.bam -I alnNeg-A147.sorted.bam -I alnNeg-A150.sorted.bam -I alnNeg-A.sorted.bam -I alnNMC-1601.sorted.bam -I alnNMC-1602.sorted.bam -I alnNMC-1603-Rp.sorted.bam -I alnNMC-1603.sorted.bam -I alnNMC-1604.sorted.bam -I alnNMC-1605.sorted.bam -I alnNMC-1606.sorted.bam -I alnNMC-1607.sorted.bam -I alnNMC-1608.sorted.bam -I alnNMC-1609.sorted.bam -I alnNMC-1610.sorted.bam -I alnNMC-1611-RpA137.sorted.bam -I alnNMC-1611.sorted.bam -I alnNMC-1612.sorted.bam -I alnNMC-1613.sorted.bam -I alnNMC-1614.sorted.bam -I alnNMC-1615.sorted.bam -I alnNMC-1616.sorted.bam -I alnNMC-1617-Rp.sorted.bam -I alnNMC-1617.sorted.bam -I alnNMC-1618.sorted.bam -I alnNMC-1619.sorted.bam -I alnNMC-1620.sorted.bam -I alnNMC-1621.sorted.bam -I alnNMC-1622.sorted.bam -I alnNMC-1623.sorted.bam -I alnNMC-1624.sorted.bam -I alnNMC-1625.sorted.bam -I alnNMC-1626.sorted.bam -I alnNMC-1627.sorted.bam -I alnNMC-1628.sorted.bam -I alnNMC-1629-Rp.sorted.bam -I alnNMC-1629.sorted.bam -I alnNMC-1630.sorted.bam -I alnNMC-1631.sorted.bam -I alnNMC-1632.sorted.bam -I alnNMC-1633.sorted.bam -I alnNMC-1634.sorted.bam -I alnNMC-1635.sorted.bam -I alnNMC-1636.sorted.bam -I alnNMC-1637.sorted.bam -I alnNMC-1638.sorted.bam -I alnNMC-1639.sorted.bam -I alnNMC-1640.sorted.bam -I alnNMC-1641.sorted.bam -I alnNMC-1642.sorted.bam -I alnNMC-1643.sorted.bam -I alnNMC-1644.sorted.bam -I alnNMC-1645.sorted.bam -I alnNMC-1646.sorted.bam -I alnNMC-1647.sorted.bam -I alnNMC-1648.sorted.bam -I alnNMC-1649.sorted.bam -I alnNMC-1650.sorted.bam -I alnNMT-1601.sorted.bam -I alnNMT-1602.sorted.bam -I alnNMT-1603.sorted.bam -I alnNMT-1604.sorted.bam -I alnNMT-1605.sorted.bam -I alnNMT-1606.sorted.bam -I alnNMT-1607.sorted.bam -I alnNMT-1608.sorted.bam -I alnNMT-1609.sorted.bam -I alnNMT-1610.sorted.bam -I alnNMT-1611.sorted.bam -I alnNMT-1612.sorted.bam -I alnNMT-1613.sorted.bam -I alnNMT-1614.sorted.bam -I alnNMT-1615.sorted.bam -I alnNMT-1616.sorted.bam -I alnNMT-1617-RpA138.sorted.bam -I alnNMT-1617.sorted.bam -I alnNMT-1618.sorted.bam -I alnNMT-1619.sorted.bam -I alnNMT-1620.sorted.bam -I alnNMT-1621-Rp.sorted.bam -I alnNMT-1621.sorted.bam -I alnNMT-1622.sorted.bam -I alnNMT-1623.sorted.bam -I alnNMT-1624.sorted.bam -I alnNMT-1625.sorted.bam -I alnNMT-1626.sorted.bam -I alnNMT-1627.sorted.bam -I alnNMT-1628.sorted.bam -I alnNMT-1629.sorted.bam -I alnNMT-1630.sorted.bam -I alnNMT-1631.sorted.bam -I alnNMT-1632.sorted.bam -I alnNMT-1633.sorted.bam -I alnNMT-1634.sorted.bam -I alnNMT-1635.sorted.bam -I alnNMT-1636.sorted.bam -I alnNMT-1637.sorted.bam -I alnNMT-1638.sorted.bam -I alnNMT-1639.sorted.bam -I alnNMT-1640.sorted.bam -I alnNMT-1641.sorted.bam -I alnNMT-1642.sorted.bam -I alnNMT-1643.sorted.bam -I alnNMT-1644.sorted.bam -I alnNMT-1645.sorted.bam -I alnNMT-1646.sorted.bam -I alnNMT-1647-Rp.sorted.bam -I alnNMT-1647.sorted.bam -I alnNMT-1648.sorted.bam -I alnNMT-1649.sorted.bam -I alnNMT-1650.sorted.bam -I alnNMT-16CW1.sorted.bam -I alnNMT-16CW2.sorted.bam -I alnNVO-1601.sorted.bam -I alnNVO-1602.sorted.bam -I alnNVO-1603.sorted.bam -I alnNVO-1604.sorted.bam -I alnNVO-1605.sorted.bam -I alnNVO-1606.sorted.bam -I alnNVO-1607.sorted.bam -I alnNVO-1608.sorted.bam -I alnNVO-1609.sorted.bam -I alnNVO-1610.sorted.bam -I alnNVO-1611.sorted.bam -I alnNVO-1612.sorted.bam -I alnNVO-1613.sorted.bam -I alnNVO-1614.sorted.bam -I alnNVO-1615.sorted.bam -I alnNVO-1616.sorted.bam -I alnNVO-1617-Rp.sorted.bam -I alnNVO-1617.sorted.bam -I alnNVO-1618.sorted.bam -I alnNVO-1619.sorted.bam -I alnNVO-1620.sorted.bam -I alnNVO-1621.sorted.bam -I alnNVO-1622.sorted.bam -I alnNVO-1623.sorted.bam -I alnNVO-1624.sorted.bam -I alnNVO-1625.sorted.bam -I alnNVO-1626.sorted.bam -I alnNVO-1627.sorted.bam -I alnNVO-1628-RpA138.sorted.bam -I alnNVO-1628.sorted.bam -I alnNVO-1629.sorted.bam -I alnNVO-1630.sorted.bam -I alnNVO-1631.sorted.bam -I alnNVO-1632.sorted.bam -I alnNVO-1633.sorted.bam -I alnNVO-1634.sorted.bam -I alnNVO-1635.sorted.bam -I alnNVO-1636.sorted.bam -I alnNVO-1637.sorted.bam -I alnNVO-1638.sorted.bam -I alnNVO-1639.sorted.bam -I alnNVO-1640.sorted.bam -I alnNVO-1641.sorted.bam -I alnNVO-1642.sorted.bam -I alnNVO-1643.sorted.bam -I alnNVO-1644.sorted.bam -I alnNVO-1645.sorted.bam -I alnNVO-1646.sorted.bam -I alnNVO-1647.sorted.bam -I alnNVO-1648.sorted.bam -I alnNVO-1649.sorted.bam -I alnNVO-1650.sorted.bam -I alnNVP-1601.sorted.bam -I alnNVP-1602.sorted.bam -I alnNVP-1603.sorted.bam -I alnNVP-1604.sorted.bam -I alnNVP-1605-RpA139.sorted.bam -I alnNVP-1605.sorted.bam -I alnNVP-1606-Rp.sorted.bam -I alnNVP-1606.sorted.bam -I alnNVP-1607.sorted.bam -I alnNVP-1608.sorted.bam -I alnNVP-1609.sorted.bam -I alnNVP-1610.sorted.bam -I alnNVP-1611.sorted.bam -I alnNVP-1612.sorted.bam -I alnNVP-1613.sorted.bam -I alnNVP-1614.sorted.bam -I alnNVP-1615.sorted.bam -I alnNVP-1616.sorted.bam -I alnNVP-1617.sorted.bam -I alnNVP-1618.sorted.bam -I alnNVP-1619.sorted.bam -I alnNVP-1620-Rp.sorted.bam -I alnNVP-1620.sorted.bam -I alnNVP-1621.sorted.bam -I alnNVP-1622.sorted.bam -I alnNVP-1623.sorted.bam -I alnNVP-1624.sorted.bam -I alnNVP-1625.sorted.bam -I alnNVP-1626.sorted.bam -I alnNVP-1627.sorted.bam -I alnNVP-1628.sorted.bam -I alnNVP-1629.sorted.bam -I alnNVP-1630.sorted.bam -I alnNVP-1631.sorted.bam -I alnNVP-1632.sorted.bam -I alnNVP-1633.sorted.bam -I alnNVP-CW1.sorted.bam -I alnORL-1601.sorted.bam -I alnORL-1602.sorted.bam -I alnORL-1603.sorted.bam -I alnORL-1604.sorted.bam -I alnORL-1605.sorted.bam -I alnORL-1606.sorted.bam -I alnORL-1607.sorted.bam -I alnORL-1608.sorted.bam -I alnORL-1609.sorted.bam -I alnORL-1610.sorted.bam -I alnORL-1611.sorted.bam -I alnORL-1612-Rp.sorted.bam -I alnORL-1612.sorted.bam -I alnORL-1613.sorted.bam -I alnORL-1614.sorted.bam -I alnORL-1615.sorted.bam -I alnORL-1616.sorted.bam -I alnORL-1617.sorted.bam -I alnORL-1618.sorted.bam -I alnORL-1619.sorted.bam -I alnORL-1620.sorted.bam -I alnORL-1621.sorted.bam -I alnORL-1622-Rp.sorted.bam -I alnORL-1622.sorted.bam -I alnORL-1623.sorted.bam -I alnORL-1624.sorted.bam -I alnORL-1625.sorted.bam -I alnORL-1626.sorted.bam -I alnORL-1627.sorted.bam -I alnORL-1628.sorted.bam -I alnORL-1629.sorted.bam -I alnORL-1630.sorted.bam -I alnORL-1631.sorted.bam -I alnORL-1632.sorted.bam -I alnORL-1633.sorted.bam -I alnORL-1634.sorted.bam -I alnORL-1635.sorted.bam -I alnORL-1636.sorted.bam -I alnORL-1637.sorted.bam -I alnORL-1638.sorted.bam -I alnORL-1639.sorted.bam -I alnORL-1640.sorted.bam -I alnORL-1641.sorted.bam -I alnORL-1642.sorted.bam -I alnORL-1643.sorted.bam -I alnORL-1644.sorted.bam -I alnORL-1645.sorted.bam -I alnORL-1646-RpA139.sorted.bam -I alnORL-1646.sorted.bam -I alnORL-1647.sorted.bam -I alnORL-1648.sorted.bam -I alnORL-1649.sorted.bam -I alnORL-1650.sorted.bam -I alnORS-1601.sorted.bam -I alnORS-1602.sorted.bam -I alnORS-1603.sorted.bam -I alnORS-1604.sorted.bam -I alnORS-1605.sorted.bam -I alnORS-1606.sorted.bam -I alnORS-1607.sorted.bam -I alnORS-1608.sorted.bam -I alnORS-1609.sorted.bam -I alnORS-1610.sorted.bam -I alnORS-1611.sorted.bam -I alnORS-1612.sorted.bam -I alnORS-1613.sorted.bam -I alnORS-1614.sorted.bam -I alnORS-1615.sorted.bam -I alnORS-1616.sorted.bam -I alnORS-1617.sorted.bam -I alnORS-1618.sorted.bam -I alnORS-1619.sorted.bam -I alnORS-1620.sorted.bam -I alnORS-1621.sorted.bam -I alnORS-1622.sorted.bam -I alnORS-1623.sorted.bam -I alnORS-1624.sorted.bam -I alnORS-1625.sorted.bam -I alnORS-1626.sorted.bam -I alnORS-1627.sorted.bam -I alnORS-1628.sorted.bam -I alnORS-1629.sorted.bam -I alnORS-1630.sorted.bam -I alnORS-1631.sorted.bam -I alnORS-1632-Rp.sorted.bam -I alnORS-1632.sorted.bam -I alnORS-1633.sorted.bam -I alnORS-1634.sorted.bam -I alnORS-1635-Rp.sorted.bam -I alnORS-1635.sorted.bam -I alnORS-1636-RpA140.sorted.bam -I alnORS-1636.sorted.bam -I alnORS-1637.sorted.bam -I alnORS-1638.sorted.bam -I alnORS-1639.sorted.bam -I alnORS-1640.sorted.bam -I alnORS-1641.sorted.bam -I alnORS-1642.sorted.bam -I alnORS-1643.sorted.bam -I alnORS-1644.sorted.bam -I alnORS-1645.sorted.bam -I alnORS-1646.sorted.bam -I alnORS-1647.sorted.bam -I alnORS-1648.sorted.bam -I alnORS-1649.sorted.bam -I alnORS-1650.sorted.bam -I alnOSO-1.sorted.bam -I alnOSO-2.sorted.bam -I alnOSO-3.sorted.bam -I alnPCI-3478-Rp.sorted.bam -I alnPCI-3478.sorted.bam -I alnPL-1302.sorted.bam -I alnPL1-A128.sorted.bam -I alnPL1-A129.sorted.bam -I alnPL1-A131.sorted.bam -I alnPL1-A133.sorted.bam -I alnPL1-A135.sorted.bam -I alnPL1-A137.sorted.bam -I alnPL1-A139.sorted.bam -I alnPL1-A141.sorted.bam -I alnPL1-A143.sorted.bam -I alnPL7-A128.sorted.bam -I alnPL7-A130.sorted.bam -I alnPL7-A132.sorted.bam -I alnPL7-A134.sorted.bam -I alnPL7-A136.sorted.bam -I alnPL7-A138.sorted.bam -I alnPL7-A140.sorted.bam -I alnPL7-A142.sorted.bam -I alnPL7-A147.sorted.bam -I alnRHF-3.sorted.bam -I alnSBR-1358.sorted.bam -I alnSBR-1360.sorted.bam -I alnSBR-1363.sorted.bam -I alnSBR-1371.sorted.bam -I alnSBR-1372.sorted.bam -I alnSFR-0243-Comp.sorted.bam -I alnSFR-0243.sorted.bam -I alnSFR-0246.sorted.bam -I alnSFR-1306.sorted.bam -I alnSFR-3366.sorted.bam -I alnSFR-3367.sorted.bam -I alnSFR-3367t.sorted.bam -I alnSFR-3369.sorted.bam -I alnSFR-3369t.sorted.bam -I alnSFR-3662.sorted.bam -I alnSFR-3663.sorted.bam -I alnSFR-3664.sorted.bam -I alnTF-5.sorted.bam -I alnTGR-0114.sorted.bam -I alnTGR-0117.sorted.bam -I alnTGR-0149-Comp.sorted.bam -I alnTGR-0149.sorted.bam -I alnTGR-0158.sorted.bam -I alnTGR-0159.sorted.bam -I alnTGR-0241.sorted.bam -I alnTGR-0250.sorted.bam -I alnTGR-0253.sorted.bam -I alnTGR-155A.sorted.bam -I alnTGR-159A.sorted.bam -I alnTGR-253E.sorted.bam -I alnTGR-2.sorted.bam -I alnTGR-3652.sorted.bam -I alnTGR-3654.sorted.bam -I alnTGR-3666.sorted.bam -I alnTGR-3.sorted.bam -I alnTGR-7932.sorted.bam -I alnTGT-0113.sorted.bam -I alnTGT-0116.sorted.bam -I alnTGT-0117.sorted.bam -I alnTGT-0119.sorted.bam -I alnTGT-0124.sorted.bam -I alnTGT-0128.sorted.bam -I alnTGT-0134.sorted.bam -I alnTGT-01.sorted.bam -I alnTGT-10.sorted.bam -I alnTWC-0112.sorted.bam -I alnTWC-0121.sorted.bam -I alnUIN-3488.sorted.bam -I alnUTB-1601.sorted.bam -I alnUTB-1602.sorted.bam -I alnUTB-1603.sorted.bam -I alnUTB-1604.sorted.bam -I alnUTB-1605.sorted.bam -I alnUTB-1606.sorted.bam -I alnUTB-1607.sorted.bam -I alnUTB-1608.sorted.bam -I alnUTB-1609.sorted.bam -I alnUTB-1610.sorted.bam -I alnUTB-1611.sorted.bam -I alnUTB-1612.sorted.bam -I alnUTB-1613.sorted.bam -I alnUTB-1614-Rp.sorted.bam -I alnUTB-1614.sorted.bam -I alnUTB-1615.sorted.bam -I alnUTB-1616.sorted.bam -I alnUTB-1617.sorted.bam -I alnUTB-1618.sorted.bam -I alnUTB-1619.sorted.bam -I alnUTB-1620.sorted.bam -I alnUTB-1621.sorted.bam -I alnUTB-1622.sorted.bam -I alnUTB-1623.sorted.bam -I alnUTB-1624.sorted.bam -I alnUTB-1625.sorted.bam -I alnUTB-1626.sorted.bam -I alnUTB-1627.sorted.bam -I alnUTB-1628.sorted.bam -I alnUTB-1629.sorted.bam -I alnUTB-1630.sorted.bam -I alnUTB-1631.sorted.bam -I alnUTB-1632.sorted.bam -I alnUTB-1633.sorted.bam -I alnUTB-1634.sorted.bam -I alnUTB-1635.sorted.bam -I alnUTB-1636.sorted.bam -I alnUTB-1637.sorted.bam -I alnUTB-1638.sorted.bam -I alnUTB-1639.sorted.bam -I alnUTB-1640.sorted.bam -I alnUTB-1641.sorted.bam -I alnUTB-1642.sorted.bam -I alnUTB-1643.sorted.bam -I alnUTB-1644.sorted.bam -I alnUTB-1645.sorted.bam -I alnUTB-1646-Rp.sorted.bam -I alnUTB-1646.sorted.bam -I alnUTB-1647.sorted.bam -I alnUTB-1648.sorted.bam -I alnUTB-1649.sorted.bam -I alnUTB-1650.sorted.bam -I alnUTK-1601.sorted.bam -I alnUTK-1602.sorted.bam -I alnUTK-1603.sorted.bam -I alnUTK-1604.sorted.bam -I alnUTK-1605.sorted.bam -I alnUTK-1606.sorted.bam -I alnUTK-1607.sorted.bam -I alnUTK-1608.sorted.bam -I alnUTK-1609.sorted.bam -I alnUTK-1610.sorted.bam -I alnUTK-1611.sorted.bam -I alnUTK-1612.sorted.bam -I alnUTK-1613.sorted.bam -I alnUTK-1614.sorted.bam -I alnUTK-1615.sorted.bam -I alnUTK-1616.sorted.bam -I alnUTK-1617.sorted.bam -I alnUTK-1618.sorted.bam -I alnUTK-1619.sorted.bam -I alnUTK-1620.sorted.bam -I alnUTK-1621.sorted.bam -I alnUTK-1622.sorted.bam -I alnUTK-1623.sorted.bam -I alnUTK-1624.sorted.bam -I alnUTK-1625.sorted.bam -I alnUTK-1626.sorted.bam -I alnUTK-1627.sorted.bam -I alnUTK-1628.sorted.bam -I alnUTK-1629.sorted.bam -I alnUTK-1630-Rp.sorted.bam -I alnUTK-1630.sorted.bam -I alnUTK-1631.sorted.bam -I alnUTK-1632.sorted.bam -I alnUTK-1633.sorted.bam -I alnUTK-1634.sorted.bam -I alnUTK-1635.sorted.bam -I alnUTK-1636.sorted.bam -I alnUTK-1637.sorted.bam -I alnUTK-1638.sorted.bam -I alnUTK-1639.sorted.bam -I alnUTK-1640.sorted.bam -I alnUTK-1641.sorted.bam -I alnUTK-1642.sorted.bam -I alnUTK-1643.sorted.bam -I alnUTK-1644.sorted.bam -I alnUTK-1645.sorted.bam -I alnUTK-1646.sorted.bam -I alnUTK-1647-Rp.sorted.bam -I alnUTK-1647.sorted.bam -I alnUTK-1648.sorted.bam -I alnUTK-1649.sorted.bam -I alnUTK-1650.sorted.bam -I alnUTM-1601.sorted.bam -I alnUTM-1602.sorted.bam -I alnUTM-1603.sorted.bam -I alnUTM-1604.sorted.bam -I alnUTM-1605.sorted.bam -I alnUTM-1606.sorted.bam -I alnUTM-1607.sorted.bam -I alnUTM-1608-RpA141.sorted.bam -I alnUTM-1608.sorted.bam -I alnUTM-1609.sorted.bam -I alnUTM-1610.sorted.bam -I alnUTM-1611.sorted.bam -I alnUTM-1612.sorted.bam -I alnUTM-1613.sorted.bam -I alnUTM-1614.sorted.bam -I alnUTM-1615.sorted.bam -I alnUTM-1616.sorted.bam -I alnUTM-1617.sorted.bam -I alnUTM-1618.sorted.bam -I alnUTM-1619.sorted.bam -I alnUTM-1620.sorted.bam -I alnUTM-1621.sorted.bam -I alnUTM-1622.sorted.bam -I alnUTM-1623.sorted.bam -I alnUTM-1624-RpA141.sorted.bam -I alnUTM-1624.sorted.bam -I alnUTM-1625.sorted.bam -I alnUTM-1626.sorted.bam -I alnUTM-1627-RpA142.sorted.bam -I alnUTM-1627.sorted.bam -I alnUTM-1628-RpA142.sorted.bam -I alnUTM-1628.sorted.bam -I alnUTM-1629-RpA142.sorted.bam -I alnUTM-1629-Rp.sorted.bam -I alnUTM-1629.sorted.bam -I alnUTM-1630.sorted.bam -I alnUTM-1631.sorted.bam -I alnUTM-1632.sorted.bam -I alnUTM-1633.sorted.bam -I alnUTM-1634.sorted.bam -I alnUTM-1635.sorted.bam -I alnUTM-1636.sorted.bam -I alnUTM-1637.sorted.bam -I alnUTM-1638.sorted.bam -I alnUTM-1639.sorted.bam -I alnUTM-1640.sorted.bam -I alnUTM-1641.sorted.bam -I alnUTM-1642.sorted.bam -I alnUTM-1643.sorted.bam -I alnUTM-1644.sorted.bam -I alnUTM-1645.sorted.bam -I alnUTM-1646.sorted.bam -I alnUTM-1647.sorted.bam -I alnUTM-1648.sorted.bam -I alnUTM-1649.sorted.bam -I alnUTM-1650.sorted.bam -I alnUTU-1601.sorted.bam -I alnUTU-1602.sorted.bam -I alnUTU-1603.sorted.bam -I alnUTU-1604.sorted.bam -I alnUTU-1605.sorted.bam -I alnUTU-1606.sorted.bam -I alnUTU-1607.sorted.bam -I alnUTU-1608.sorted.bam -I alnUTU-1609.sorted.bam -I alnUTU-1610.sorted.bam -I alnUTU-1611.sorted.bam -I alnUTU-1612.sorted.bam -I alnUTU-1613-RpA142.sorted.bam -I alnUTU-1613.sorted.bam -I alnUTU-1614.sorted.bam -I alnUTU-1615.sorted.bam -I alnUTU-1616.sorted.bam -I alnUTU-1617.sorted.bam -I alnUTU-1618.sorted.bam -I alnUTU-1619.sorted.bam -I alnUTU-1620.sorted.bam -I alnUTU-1621.sorted.bam -I alnUTU-1622.sorted.bam -I alnUTU-1623.sorted.bam -I alnUTU-1624.sorted.bam -I alnUTU-1625.sorted.bam -I alnUTU-1626.sorted.bam -I alnUTU-1627.sorted.bam -I alnUTU-1628.sorted.bam -I alnUTU-1629.sorted.bam -I alnUTU-1630.sorted.bam -I alnUTU-1631.sorted.bam -I alnUTU-1632.sorted.bam -I alnUTU-1633.sorted.bam -I alnUTU-1634.sorted.bam -I alnUTU-1635.sorted.bam -I alnUTU-163613A.sorted.bam -I alnUTU-1636.sorted.bam -I alnUTU-1637.sorted.bam -I alnUTU-1638.sorted.bam -I alnUTU-1639.sorted.bam -I alnUTU-1640-Rp.sorted.bam -I alnUTU-1640.sorted.bam -I alnUTU-1641.sorted.bam -I alnUTU-1642.sorted.bam -I alnUTU-1643.sorted.bam -I alnUTU-1644.sorted.bam -I alnUTU-1645.sorted.bam -I alnUTU-1646.sorted.bam -I alnUTU-1647.sorted.bam -I alnUTU-1648.sorted.bam -I alnUTU-1649.sorted.bam -I alnUTU-1650.sorted.bam -I alnUTW-1601.sorted.bam -I alnUTW-1602-RpA142.sorted.bam -I alnUTW-1602.sorted.bam -I alnUTW-1603.sorted.bam -I alnUTW-1604.sorted.bam -I alnUTW-1605.sorted.bam -I alnUTW-1606.sorted.bam -I alnUTW-1607.sorted.bam -I alnUTW-1608.sorted.bam -I alnUTW-1609.sorted.bam -I alnUTW-1610.sorted.bam -I alnUTW-1611.sorted.bam -I alnUTW-1612.sorted.bam -I alnUTW-1613.sorted.bam -I alnUTW-1614-Rp.sorted.bam -I alnUTW-1614.sorted.bam -I alnUTW-1615.sorted.bam -I alnUTW-1616.sorted.bam -I alnUTW-1617.sorted.bam -I alnUTW-1618.sorted.bam -I alnUTW-1619.sorted.bam -I alnUTW-1620.sorted.bam -I alnUTW-1621.sorted.bam -I alnUTW-1622.sorted.bam -I alnUTW-1623-Rp.sorted.bam -I alnUTW-1623.sorted.bam -I alnUTW-1624.sorted.bam -I alnUTW-1625.sorted.bam -I alnUTW-1626.sorted.bam -I alnUTW-1627.sorted.bam -I alnUTW-1628.sorted.bam -I alnUTW-1629.sorted.bam -I alnUTW-1630-Rp.sorted.bam -I alnUTW-1630.sorted.bam -I alnUTW-1631.sorted.bam -I alnUTW-1632.sorted.bam -I alnUTW-1633.sorted.bam -I alnUTW-1634.sorted.bam -I alnUTW-1635.sorted.bam -I alnUTW-1636.sorted.bam -I alnUTW-1637-RpA143.sorted.bam -I alnUTW-1637.sorted.bam -I alnUTW-1638.sorted.bam -I alnUTW-1639.sorted.bam -I alnUTW-1640.sorted.bam -I alnUTW-1641.sorted.bam -I alnUTW-1642.sorted.bam -I alnUTW-1643.sorted.bam -I alnUTW-1644.sorted.bam -I alnUTW-1645.sorted.bam -I alnUTW-1646.sorted.bam -I alnUTW-1647.sorted.bam -I alnUTW-1648.sorted.bam -I alnUTW-1649.sorted.bam -I alnUTW-1650.sorted.bam -I alnWCR-1341-Comp.sorted.bam -I alnWCR-1341.sorted.bam -I alnWCR-1342-Comp.sorted.bam -I alnWCR-1342.sorted.bam -I alnWYB-1601.sorted.bam -I alnWYB-1602.sorted.bam -I alnWYB-1603.sorted.bam -I alnWYB-1604.sorted.bam -I alnWYB-1605.sorted.bam -I alnWYB-1606.sorted.bam -I alnWYB-1607.sorted.bam -I alnWYB-1608.sorted.bam -I alnWYB-1609.sorted.bam -I alnWYB-1610.sorted.bam -I alnWYB-1611.sorted.bam -I alnWYB-1612-RpA143.sorted.bam -I alnWYB-1612.sorted.bam -I alnWYB-1613.sorted.bam -I alnWYB-1614.sorted.bam -I alnWYB-1615.sorted.bam -I alnWYB-1616.sorted.bam -I alnWYB-1617.sorted.bam -I alnWYB-1618.sorted.bam -I alnWYB-1619.sorted.bam -I alnWYB-1620.sorted.bam -I alnWYB-1621.sorted.bam -I alnWYB-1622.sorted.bam -I alnWYB-1623.sorted.bam -I alnWYB-1624.sorted.bam -I alnWYB-1625.sorted.bam -I alnWYB-1626.sorted.bam -I alnWYB-1627.sorted.bam -I alnWYB-1628.sorted.bam -I alnWYB-1629.sorted.bam -I alnWYB-1630.sorted.bam -I alnWYB-1631.sorted.bam -I alnWYB-1632.sorted.bam -I alnWYB-1633.sorted.bam -I alnWYB-1634.sorted.bam -I alnWYB-1635.sorted.bam -I alnWYB-1636.sorted.bam -I alnWYB-1637.sorted.bam -I alnWYB-1638.sorted.bam -I alnWYB-1639.sorted.bam -I alnWYB-1640.sorted.bam -I alnWYB-1641.sorted.bam -I alnWYB-1642.sorted.bam -I alnWYB-1643.sorted.bam -I alnWYB-1644.sorted.bam -I alnWYB-1645.sorted.bam -I alnWYB-1646.sorted.bam -I alnWYB-1647.sorted.bam -I alnWYB-1648.sorted.bam -I alnWYB-1649.sorted.bam -I alnWYB-1650-Rp.sorted.bam -I alnWYB-1650.sorted.bam -I alnWYW-1601.sorted.bam -I alnWYW-1602.sorted.bam -I alnWYW-1603-Rp.sorted.bam -I alnWYW-1603.sorted.bam -I alnWYW-1604.sorted.bam -I alnWYW-1605.sorted.bam -I alnWYW-1606-Rp.sorted.bam -I alnWYW-1606.sorted.bam -I alnWYW-1607.sorted.bam -I alnWYW-1608.sorted.bam -I alnWYW-1609.sorted.bam -I alnWYW-1610.sorted.bam -I alnWYW-1611.sorted.bam -I alnWYW-1612.sorted.bam -I alnWYW-1613.sorted.bam -I alnWYW-1614.sorted.bam -I alnWYW-1615.sorted.bam -I alnWYW-1616.sorted.bam -I alnWYW-1617.sorted.bam -I alnWYW-1618.sorted.bam -I alnWYW-1619.sorted.bam -I alnWYW-1620.sorted.bam -I alnWYW-1621.sorted.bam -I alnWYW-1622.sorted.bam -I alnWYW-1623.sorted.bam -I alnWYW-1624.sorted.bam -I alnWYW-1625.sorted.bam -I alnWYW-1626.sorted.bam -I alnWYW-1627.sorted.bam -I alnWYW-1628.sorted.bam -I alnWYW-1629.sorted.bam -I alnWYW-1630-RpA128.sorted.bam -I alnWYW-1630.sorted.bam -I alnWYW-1631.sorted.bam -I alnWYW-1632.sorted.bam -I alnWYW-1633.sorted.bam -I alnWYW-1634.sorted.bam -I alnWYW-1635.sorted.bam -I alnWYW-1636.sorted.bam -I alnWYW-1637.sorted.bam -I alnWYW-1638.sorted.bam -I alnWYW-1639.sorted.bam -I alnWYW-1640.sorted.bam -I alnWYW-1641.sorted.bam -I alnWYW-1642.sorted.bam -I alnWYW-1643.sorted.bam -I alnWYW-1644.sorted.bam -I alnWYW-1645.sorted.bam -I alnWYW-1646.sorted.bam -I alnWYW-1647-RpA147.sorted.bam -I alnWYW-1647.sorted.bam -I alnWYW-1648.sorted.bam -I alnWYW-1649.sorted.bam -I alnWYW-1650.sorted.bam

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