SRR5088801 dbb76854faeb6cdde9ab4f34c577c0bc none NIL bwa mem 0.7.7-r441 1000 Genomes hs37d5 reference sequence new none Picard (varies) yes new GATK IndelRealigner 3.3 knownAlleles=[ (RodBinding name=knownAlleles source=Homo_sapiens_assembly19.dbsnp.vcf), (RodBinding name=knownAlleles2 source=Homo_sapiens_assembly19.known_indels.vcf), (RodBinding name=knownAlleles3 source=Homo_sapiens_assembly19.variantEvalGoldStandard.vcf)], targetIntervals = sample-specific old yes GATK BaseRecalibrator 3.3 --useOriginalQualities -knownSites Homo_sapiens_assembly19.dbsnp.vcf -knownSites Homo_sapiens_assembly19.known_indels.vcf -knownSites Homo_sapiens_assembly19.variantEvalGoldStandard.vcf done old bamUtils squeeze 1.0.13 --keepDups --binMid --binQualS 2,3,10,20,25,30,35,40,50 home done samtools view -C 1.3.1 Using htslib 1.3.1 genome reference sequence retrieved from: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz assembly GRCh37 options --defer-secondary