Post date: Feb 18, 2017 5:17:16 AM
The alignments are in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tsp/.
Here is what I did:
1. Remove PCR duplicates for 252 bam files (84 individuals). This requires loading java (jdk/1.8.0_25).
perl markDups.pl aln_[0-9]_*sorted.bam
example
java -Xmx96g -jar /uufs/chpc.utah.edu/sys/installdir/picard/2.1.1/picard.jar MarkDuplicates INPUT=aln_3_podu_PCT_WP_2934-hcfBVlhF.sorted.bam OUTPUT=aln_3_podu_PCT_WP_2934-hcfBVlhF.dedup.bam METRICS_FILE=aln_3_podu_PCT_WP_2934-hcfBVlhF.dedup.log.txt
2. Generate g.vcf files for each individual.
perl ../scripts/wrap_qsub_slurm_gatk.pl files_*
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tsp
java -Xmx48g -jar ~/bin/GenomeAnalysisTK.jar -T HaplotypeCaller -R /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta -I /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/alignments_tsp/files_podu_PCT_WP_2934.list -o /scratch/general/lustre/timemasGatk/podu_PCT_WP_2934.g.vcf -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
cp /scratch/general/lustre/timemasGatk/podu_PCT_WP_2934.g.vcf /uufs/chpc.utah.edu/common/home/u6000989/data/timema/combind_wgs_dovetailV3/variants_tsp/podu_PCT_WP_2934.g.vcf
NEED TO FIX LG IDS