This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
GenotypeGVCFs sample specific genotype columns
Hi, I have generated 9 .g.vcf files from my .bam files, and want to do joint genotype calling with all these gvcf files using GenotypeGVCFs tool. I have the following command:
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R ref.fasta -V:VCF gvcflist.list -o output.vcf
In my output, I expected to find 9 sample columns for the genotype (ie 0/1:195,32:250:99:534,0,6705), however I can only find one sample column in the vcf file, and it seems that all 9 samples were pooled together. May I know if I have done something wrong? I would like to know individual genotype for each sample.
I have tried to use:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -I sam1.bam -I sam2.bam -I sam3.bam ....
and also only obtain one column instead of multiple-sample column for the genotype.