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multi-vcf file using UnifiedGenotyper

PolaPola IsraelMember
edited August 2014 in Ask the GATK team

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

Pola

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