Test-drive the GATK tools and Best Practices pipelines on Terra
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SampleList annotation returns only one sample while being used in a variant call on two samples
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