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Missing variants from vcf to gvcf
I work with complete sequences of Y chromosome of NGS. I'm creating a GVCF multisample from 24 single vcfs. Once I created the GVCF multisample, I realize that for 11 samples I'm missing variants. As seen in the example, from column 10 to 20 shouldn't give 0 since it's a variant present in the singles vcfs of those samples. What might be going wrong?
Y 28670117 . T C 9746.79 . AC=12;AF=1.00;AN=12;DP=239;FS=0.000;MLEAC=12;MLEAF=1.00;MQ=59.41;QD=31.70;SOR=0.894 GT:AD:DP:GQ:PL .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 .:0,0 1:0,10:10:99:322,0 1:0,20:20:99:853,0 1:0,22:22:99:916,0 1:0,25:25:99:1023,0 1:0,25:25:99:1041,0 1:0,18:18:99:749,0 1:0,36:36:99:1418,0 1:0,12:12:99:523,0 1:0,30:30:99:310,0 1:0,9:9:99:294,0 1:0,3:3:99:105,0 1:0,28:28:99:1217,0.:0,0
This is the command that I used:
java -jar /home/GATK/GenomeAnalysisTK.jar -R /home/hgref_human_b37_ChrY/human_g1k_v37_decoy.fasta -T GenotypeGVCFs -o S.genotypeGVCF.vcf -allSites --variant sample1.haplotypecallerGVCF.g.vcf --variant sample2.haplotypecallerGVCF.g.vcf --variant allsamples.haplotypecallerGVCF.g.vcf > S.genotypeGVCF.log 2>&1