SRR3091456 621b12745ee99bc4db95aaf656b5a90d none NIL bwa mem 0.7.10-r789 new none Picard 1.111 yes new GATK IndelRealigner 3.2-2 knownAlleles = dbSNP138.vcf, targetIntervals = sample-specific old yes GATK BaseRecalibrator 3.2-2 [ ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate ] done old bamUtils squeeze 1.0.13 --keepDups --binMid --binQualS 2,3,10,20,25,30,35,40,50 home done samtools view -C 1.2 Using htslib 1.2.1 genome reference sequence retrieved from: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz assembly GRCh37 Alignment Provider Sequencing Center