Post date: Jun 25, 2018 10:25:7 PM
We had not yet aligned the T. cristinae whole genome data from the natural pouplations to the Devetail version 3 genome. This is taking place in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tcr/. There are 160 individuals from four populations pairs (eight populations).
1. Get correct ids. Run perl combineIdFields.pl. Needed to fix two manually because of weirdness in ~/data/timema/timema_wgrs/sequencing-submission-form-P130133_stick_insect_Q130022.ods.
Generates idsPlus.txt.
The first column is the numerical ID, this is followed by two columns with population/individual data, then the plate and sequence ID number (matches the fastq files).
2. Run the alignments with bwa mem (version 0.7.17-r1188). Note that there are four runs for each sample (with two files each).
From /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tcr/
perl ../scripts/wrap_qsub_slurm_bwa-wgs-wild.pl
Here is an example command.
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tcr/
bwa mem -t 8 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:timemaR12C_10221021-69603\tPL:ILLUMINA\tLB:timemaR12C_10221021\tSM:timemaR12C_10221021' /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/re_mod_map_timema_06Jun2016_RvNkF702.fasta /uufs/chpc.utah.edu/common/home/u6000989/data/timema/timema_wgrs/plate6/WTCHG_69603_272_1.fastq /uufs/chpc.utah.edu/common/home/u6000989/data/timema/timema_wgrs/plate6/WTCHG_69603_272_2.fastq > /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tcr/aln_6_69603_timemaR12C_10221021.sam 2> /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tcr/error_6_69603_timemaR12C_10221021.log
3. As an interactive job, compress, sort and index sam files, then remove PCR duplicates and re-index the bam alignments.
First, run Sam2BamFork.pl on the sam files (this runs samtools 1.5 with htslib 1.5).
#!/usr/bin/perl
#
# conver sam to bam, then sort and index
#
use Parallel::ForkManager;
my $max = 24;
my $pm = Parallel::ForkManager->new($max);
FILES:
foreach $sam (@ARGV){
$pm->start and next FILES; ## fork
$sam =~ m/^([A-Za-z0-9_\-]+\.)sam/ or die "failed to match $fq\n";
$base = $1;
system "samtools view -b -O BAM -o $base"."bam $sam\n";
system "samtools sort -O BAM -o $base"."sorted.bam $base"."bam\n";
system "samtools index -b $base"."sorted.bam\n";
$pm->finish;
}
$pm->wait_all_children;
Then run RmdupFork.pl on the *sorted.bam files (also samtools 1.5, rmdup command).
#!/usr/bin/perl
#
# removes pcr duplicates
#
use Parallel::ForkManager;
my $max = 24;
my $pm = Parallel::ForkManager->new($max);
FILES:
foreach $bam (@ARGV){
$pm->start and next FILES; ## fork
$ubam = $bam;
$ubam =~ s/sorted/uniqe/ or die "failed sub $ubam\n";
system "samtools rmdup -S $bam $ubam\n";
system "samtools index -b $ubam\n";
$pm->finish;
}
$pm->wait_all_children;
4. Alignments with HaplotypeCaller, g.vcf format. I am hoping that samples can be merged during joint calling! I ran the HaplotypeCaller on each *bam file to generate g.vcf files. I did this with ../scripts/wrap_qsub_slurm_gatk.pl. Here are the key commands:
## build array of jobs to be run individually (serially) by slurm
my $idir = '/uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tsp';
my $odir = '/uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/variants_tsp';
my $tdir = '/scratch/general/lustre/timemasGatk';
my @jobarray;
my $hapcall;
my $out;
my $genome = "/uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta";
my $cd = "cd $idir\n";
## files are the bam lists
foreach my $file (@ARGV){
chomp($file);
$out = $file;
$out =~ s/files_// or die "failed here: $out\n";
$out =~ s/list/g.vcf/ or die "failed here: $out\n";
$hapcall = "java -Xmx48g -jar ~/bin/GenomeAnalysisTK.jar -T HaplotypeCaller -R $genome -I $idir/$file -o $tdir/$out -gt_mode DISCOVERY -hets 0.001 -mbq 30 -out_mode EMIT_VARIANTS_ONLY -ploidy 2 -stand_call_conf 50 -pcrModel AGGRESSIVE --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000\ncp $tdir/$out $odir/$out\n";
push (@jobarray, "$cd"."$hapcall");
print "$cd"."$hapcall";
}
Next, I combined sets of 96 g.vcf files. This is done as a batch submission with combine_GVCFs.sh.
#!/bin/sh
#SBATCH --time=200:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=24
#SBATCH --account=gompert-kp
#SBATCH --partition=gompert-kp
#SBATCH --job-name=gatk
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=zach.gompert@usu.edu
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/variants_tcr
perl runCombineGVCFs.pl
Here is the perl script it runs:
#!/usr/bin/perl
# fix scaffold names
use Parallel::ForkManager;
my $max = 10;
my $pm = Parallel::ForkManager->new($max);
open(IN,"jobs.txt") or die;
while(<IN>){
push(@jobs,$_);
}
FILES:
foreach $job (@jobs){
$pm->start and next FILES; ## fork
print "JOB=$job\n\n";
system "$job\n";
$pm->finish;
}
$pm->wait_all_children;
And jobs.txt, which as the individual jobs (sets of 96 samples)
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_5_67064_timemaHVA_8021022.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021024.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021027.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021028.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021029.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021030.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021034.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021035.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021037.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021039.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8021040.uniqe.g.vcf --variant aln_5_67064_timemaHVA_8091009.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021001.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021002.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021003.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021004.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021005.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021010.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021011.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021012.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021013.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021014.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021015.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021019.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8021020.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8101011.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8101012.uniqe.g.vcf --variant aln_5_67064_timemaHVC_8101013.uniqe.g.vcf --variant aln_5_67064_timemaLA_10160904.uniqe.g.vcf --variant aln_5_67064_timemaLA_10160906.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070901.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070903.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070904.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070905.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070906.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070907.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070908.uniqe.g.vcf --variant aln_5_67064_timemaLA_12070910.uniqe.g.vcf --variant aln_5_67064_timemaLA_4091006.uniqe.g.vcf --variant aln_5_67064_timemaLA_4091007.uniqe.g.vcf --variant aln_5_67064_timemaLA_4091008.uniqe.g.vcf --variant aln_5_67064_timemaLA_4091009.uniqe.g.vcf --variant aln_5_67064_timemaLA_4091010.uniqe.g.vcf --variant aln_5_67064_timemaLA_4091012.uniqe.g.vcf --variant aln_5_67064_timemaMR1A_8051001.uniqe.g.vcf --variant aln_5_67064_timemaMR1A_8051002.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010901.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010902.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010903.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010904.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010905.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010906.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010907.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010908.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010909.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010910.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010911.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12010912.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12070912.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12070913.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12070915.uniqe.g.vcf --variant aln_5_67064_timemaPRC_12070916.uniqe.g.vcf --variant aln_5_67064_timemaPRC_4091002.uniqe.g.vcf --variant aln_5_67064_timemaPRC_4091003.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021022.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021024.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021027.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021028.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021029.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021030.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021034.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021035.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021037.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021039.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8021040.uniqe.g.vcf --variant aln_5_67694_timemaHVA_8091009.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021001.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021002.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021003.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021004.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021005.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021010.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021011.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021012.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021013.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021014.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021015.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021019.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8021020.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8101011.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8101012.uniqe.g.vcf --variant aln_5_67694_timemaHVC_8101013.uniqe.g.vcf --variant aln_5_67694_timemaLA_10160904.uniqe.g.vcf --variant aln_5_67694_timemaLA_10160906.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070901.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070903.uniqe.g.vcf -o combinded_1.g.vcf
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_5_67694_timemaLA_12070904.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070905.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070906.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070907.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070908.uniqe.g.vcf --variant aln_5_67694_timemaLA_12070910.uniqe.g.vcf --variant aln_5_67694_timemaLA_4091006.uniqe.g.vcf --variant aln_5_67694_timemaLA_4091007.uniqe.g.vcf --variant aln_5_67694_timemaLA_4091008.uniqe.g.vcf --variant aln_5_67694_timemaLA_4091009.uniqe.g.vcf --variant aln_5_67694_timemaLA_4091010.uniqe.g.vcf --variant aln_5_67694_timemaLA_4091012.uniqe.g.vcf --variant aln_5_67694_timemaMR1A_8051001.uniqe.g.vcf --variant aln_5_67694_timemaMR1A_8051002.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010901.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010902.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010903.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010904.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010905.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010906.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010907.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010908.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010909.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010910.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010911.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12010912.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12070912.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12070913.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12070915.uniqe.g.vcf --variant aln_5_67694_timemaPRC_12070916.uniqe.g.vcf --variant aln_5_67694_timemaPRC_4091002.uniqe.g.vcf --variant aln_5_67694_timemaPRC_4091003.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021022.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021024.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021027.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021028.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021029.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021030.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021034.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021035.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021037.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021039.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8021040.uniqe.g.vcf --variant aln_5_67879_timemaHVA_8091009.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021001.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021002.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021003.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021004.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021005.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021010.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021011.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021012.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021013.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021014.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021015.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021019.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8021020.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8101011.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8101012.uniqe.g.vcf --variant aln_5_67879_timemaHVC_8101013.uniqe.g.vcf --variant aln_5_67879_timemaLA_10160904.uniqe.g.vcf --variant aln_5_67879_timemaLA_10160906.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070901.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070903.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070904.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070905.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070906.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070907.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070908.uniqe.g.vcf --variant aln_5_67879_timemaLA_12070910.uniqe.g.vcf --variant aln_5_67879_timemaLA_4091006.uniqe.g.vcf --variant aln_5_67879_timemaLA_4091007.uniqe.g.vcf --variant aln_5_67879_timemaLA_4091008.uniqe.g.vcf --variant aln_5_67879_timemaLA_4091009.uniqe.g.vcf --variant aln_5_67879_timemaLA_4091010.uniqe.g.vcf --variant aln_5_67879_timemaLA_4091012.uniqe.g.vcf --variant aln_5_67879_timemaMR1A_8051001.uniqe.g.vcf --variant aln_5_67879_timemaMR1A_8051002.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010901.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010902.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010903.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010904.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010905.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010906.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010907.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010908.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010909.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010910.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010911.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12010912.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12070912.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12070913.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12070915.uniqe.g.vcf --variant aln_5_67879_timemaPRC_12070916.uniqe.g.vcf --variant aln_5_67879_timemaPRC_4091002.uniqe.g.vcf --variant aln_5_67879_timemaPRC_4091003.uniqe.g.vcf -o combinded_2.g.vcf
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_5_68110_timemaHVA_8021022.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021024.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021027.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021028.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021029.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021030.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021034.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021035.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021037.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021039.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8021040.uniqe.g.vcf --variant aln_5_68110_timemaHVA_8091009.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021001.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021002.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021003.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021004.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021005.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021010.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021011.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021012.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021013.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021014.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021015.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021019.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8021020.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8101011.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8101012.uniqe.g.vcf --variant aln_5_68110_timemaHVC_8101013.uniqe.g.vcf --variant aln_5_68110_timemaLA_10160904.uniqe.g.vcf --variant aln_5_68110_timemaLA_10160906.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070901.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070903.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070904.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070905.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070906.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070907.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070908.uniqe.g.vcf --variant aln_5_68110_timemaLA_12070910.uniqe.g.vcf --variant aln_5_68110_timemaLA_4091006.uniqe.g.vcf --variant aln_5_68110_timemaLA_4091007.uniqe.g.vcf --variant aln_5_68110_timemaLA_4091008.uniqe.g.vcf --variant aln_5_68110_timemaLA_4091009.uniqe.g.vcf --variant aln_5_68110_timemaLA_4091010.uniqe.g.vcf --variant aln_5_68110_timemaLA_4091012.uniqe.g.vcf --variant aln_5_68110_timemaMR1A_8051001.uniqe.g.vcf --variant aln_5_68110_timemaMR1A_8051002.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010901.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010902.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010903.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010904.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010905.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010906.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010907.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010908.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010909.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010910.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010911.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12010912.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12070912.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12070913.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12070915.uniqe.g.vcf --variant aln_5_68110_timemaPRC_12070916.uniqe.g.vcf --variant aln_5_68110_timemaPRC_4091002.uniqe.g.vcf --variant aln_5_68110_timemaPRC_4091003.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8021026.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8021038.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8091001.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8091002.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8091003.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8091004.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8091005.uniqe.g.vcf --variant aln_6_67065_timemaHVA_8091010.uniqe.g.vcf --variant aln_6_67065_timemaHVC_8021008.uniqe.g.vcf --variant aln_6_67065_timemaHVC_8021009.uniqe.g.vcf --variant aln_6_67065_timemaHVC_8021016.uniqe.g.vcf --variant aln_6_67065_timemaHVC_8021018.uniqe.g.vcf --variant aln_6_67065_timemaLA_12070902.uniqe.g.vcf --variant aln_6_67065_timemaLA_12070911.uniqe.g.vcf --variant aln_6_67065_timemaLA_4091005.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051003.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051004.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051005.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051006.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051007.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051008.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051009.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051010.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051011.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051012.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051014.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051017.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051018.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051019.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051020.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051021.uniqe.g.vcf --variant aln_6_67065_timemaMR1A_8051022.uniqe.g.vcf -o combinded_3.g.vcf
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_6_67065_timemaMR1A_8051023.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111003.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111004.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111006.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111007.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111008.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111009.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111010.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111011.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111012.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111013.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111014.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111015.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111017.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111018.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111019.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111020.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111021.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111022.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111023.uniqe.g.vcf --variant aln_6_67065_timemaMR1C_8111024.uniqe.g.vcf --variant aln_6_67065_timemaPRC_12070914.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201001.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201002.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201003.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201004.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201005.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201006.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201007.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201008.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201009.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201010.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201011.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201012.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201013.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201014.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201015.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201016.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201017.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201018.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201019.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201020.uniqe.g.vcf --variant aln_6_67065_timemaR12A_10201021.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221001.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221002.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221003.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221004.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221005.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221006.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221007.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221008.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221009.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221010.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221011.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221012.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221013.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221014.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221015.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221016.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221017.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221018.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221019.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221020.uniqe.g.vcf --variant aln_6_67065_timemaR12C_10221021.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8021026.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8021038.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8091001.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8091002.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8091003.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8091004.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8091005.uniqe.g.vcf --variant aln_6_67880_timemaHVA_8091010.uniqe.g.vcf --variant aln_6_67880_timemaHVC_8021008.uniqe.g.vcf --variant aln_6_67880_timemaHVC_8021009.uniqe.g.vcf --variant aln_6_67880_timemaHVC_8021016.uniqe.g.vcf --variant aln_6_67880_timemaHVC_8021018.uniqe.g.vcf --variant aln_6_67880_timemaLA_12070902.uniqe.g.vcf --variant aln_6_67880_timemaLA_12070911.uniqe.g.vcf --variant aln_6_67880_timemaLA_4091005.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051003.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051004.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051005.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051006.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051007.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051008.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051009.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051010.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051011.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051012.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051014.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051017.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051018.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051019.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051020.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051021.uniqe.g.vcf --variant aln_6_67880_timemaMR1A_8051022.uniqe.g.vcf -o combinded_4.g.vcf
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_6_67880_timemaMR1A_8051023.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111003.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111004.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111006.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111007.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111008.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111009.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111010.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111011.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111012.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111013.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111014.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111015.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111017.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111018.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111019.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111020.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111021.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111022.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111023.uniqe.g.vcf --variant aln_6_67880_timemaMR1C_8111024.uniqe.g.vcf --variant aln_6_67880_timemaPRC_12070914.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201001.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201002.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201003.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201004.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201005.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201006.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201007.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201008.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201009.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201010.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201011.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201012.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201013.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201014.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201015.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201016.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201017.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201018.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201019.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201020.uniqe.g.vcf --variant aln_6_67880_timemaR12A_10201021.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221001.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221002.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221003.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221004.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221005.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221006.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221007.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221008.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221009.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221010.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221011.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221012.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221013.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221014.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221015.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221016.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221017.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221018.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221019.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221020.uniqe.g.vcf --variant aln_6_67880_timemaR12C_10221021.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8021026.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8021038.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8091001.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8091002.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8091003.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8091004.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8091005.uniqe.g.vcf --variant aln_6_68111_timemaHVA_8091010.uniqe.g.vcf --variant aln_6_68111_timemaHVC_8021008.uniqe.g.vcf --variant aln_6_68111_timemaHVC_8021009.uniqe.g.vcf --variant aln_6_68111_timemaHVC_8021016.uniqe.g.vcf --variant aln_6_68111_timemaHVC_8021018.uniqe.g.vcf --variant aln_6_68111_timemaLA_12070902.uniqe.g.vcf --variant aln_6_68111_timemaLA_12070911.uniqe.g.vcf --variant aln_6_68111_timemaLA_4091005.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051003.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051004.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051005.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051006.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051007.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051008.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051009.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051010.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051011.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051012.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051014.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051017.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051018.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051019.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051020.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051021.uniqe.g.vcf --variant aln_6_68111_timemaMR1A_8051022.uniqe.g.vcf -o combinded_5.g.vcf
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_6_68111_timemaMR1A_8051023.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111003.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111004.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111006.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111007.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111008.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111009.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111010.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111011.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111012.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111013.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111014.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111015.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111017.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111018.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111019.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111020.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111021.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111022.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111023.uniqe.g.vcf --variant aln_6_68111_timemaMR1C_8111024.uniqe.g.vcf --variant aln_6_68111_timemaPRC_12070914.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201001.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201002.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201003.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201004.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201005.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201006.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201007.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201008.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201009.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201010.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201011.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201012.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201013.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201014.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201015.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201016.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201017.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201018.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201019.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201020.uniqe.g.vcf --variant aln_6_68111_timemaR12A_10201021.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221001.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221002.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221003.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221004.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221005.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221006.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221007.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221008.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221009.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221010.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221011.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221012.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221013.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221014.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221015.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221016.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221017.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221018.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221019.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221020.uniqe.g.vcf --variant aln_6_68111_timemaR12C_10221021.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8021026.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8021038.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8091001.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8091002.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8091003.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8091004.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8091005.uniqe.g.vcf --variant aln_6_69603_timemaHVA_8091010.uniqe.g.vcf --variant aln_6_69603_timemaHVC_8021008.uniqe.g.vcf --variant aln_6_69603_timemaHVC_8021009.uniqe.g.vcf --variant aln_6_69603_timemaHVC_8021016.uniqe.g.vcf --variant aln_6_69603_timemaHVC_8021018.uniqe.g.vcf --variant aln_6_69603_timemaLA_12070902.uniqe.g.vcf --variant aln_6_69603_timemaLA_12070911.uniqe.g.vcf --variant aln_6_69603_timemaLA_4091005.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051003.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051004.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051005.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051006.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051007.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051008.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051009.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051010.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051011.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051012.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051014.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051017.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051018.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051019.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051020.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051021.uniqe.g.vcf --variant aln_6_69603_timemaMR1A_8051022.uniqe.g.vcf -o combinded_6.g.vcf
java -Xmx80g -jar ~/bin/GenomeAnalysisTK.jar -T CombineGVCFs -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta --variant aln_6_69603_timemaMR1A_8051023.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111003.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111004.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111006.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111007.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111008.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111009.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111010.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111011.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111012.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111013.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111014.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111015.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111017.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111018.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111019.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111020.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111021.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111022.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111023.uniqe.g.vcf --variant aln_6_69603_timemaMR1C_8111024.uniqe.g.vcf --variant aln_6_69603_timemaPRC_12070914.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201001.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201002.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201003.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201004.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201005.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201006.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201007.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201008.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201009.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201010.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201011.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201012.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201013.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201014.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201015.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201016.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201017.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201018.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201019.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201020.uniqe.g.vcf --variant aln_6_69603_timemaR12A_10201021.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221001.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221002.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221003.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221004.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221005.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221006.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221007.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221008.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221009.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221010.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221011.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221012.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221013.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221014.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221015.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221016.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221017.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221018.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221019.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221020.uniqe.g.vcf --variant aln_6_69603_timemaR12C_10221021.uniqe.g.vcf
5.