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multi-vcf file using UnifiedGenotyper
I am new to GATK , I am trying to analyze the exome of 3 family members. I followed GATK v2.8 recommendations and generated 3 bam files which were then used as input to UnifiedGenotyper using the command below:
java -jar /opt/software/GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ucsc.hg19.fasta -I output133.bam -I recal134.bam -I recal135.bam -stand_emit_conf 10 -stand_call_conf 50 -dcov 200 -A AlleleBalance -A QualByDepth -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A RMSMappingQuality -A Coverage -o temp.vcf
When looking at the output "temp.vcf" I realized that its not multi-vcf file, but rather describes the genotype of a single sample.
Below are few lines from the vcf file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 133
chrM 73 . G A 588.77 . ABHet=0.350;AC=1;AF=0.500;AN=2;BaseQRankSum=-0.440;DP=40;Dels=0.00;FS=5.942;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=0.354;QD=14.72;ReadPosRankSum=0.780 GT:AD:DP:GQ:PL 0/1:14,26:40:99:617,0,385 chrM 150 . T C 1118.77 . ABHom=1.00;AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.90 GT:AD:DP:GQ:PL 1/1:0,34:34:93:1147,93,0
Any suggestion ?
Thank you for your help