To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

SampleList annotation returns only one sample while being used in a variant call on two samples

Hi there,

I have used HaplotypeCaller from GATK4 to call variants on two affected siblings. I put SampleList annotation in the command but only one sample is seen in all of the variants in the resulting VCF file.
Mind you I have done this before on GATK 3x versions and never had such a problem. I could use the "set" column to see variants regarding each sample easily.

gatk HaplotypeCaller \ -R ~/Arvand/hg19/ucsc.hg19.fasta \ -I ~/Arvand/5137D_recalibrated.bam \ -I ~/Arvand/5137E_recalibrated.bam -O affected_raw.vcf.gz \ -bamout affected_bamout.bam -A BaseQuality -A ChromosomeCounts -A Coverage -A DepthPerAlleleBySample -A RMSMappingQuality -A OxoGReadCounts -A QualByDepth -A FisherStrand -A StrandOddsRatio -A SampleList --genotyping-mode DISCOVERY -D ~/Arvand/hg19/dbsnp_147.hg19.vcf.gz --native-pair-hmm-threads 20


Best Answer


Sign In or Register to comment.