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select private SNPs for individual samples from a multisample VCF

jfmunozjfmunoz Broad InstituteMember

I'm trying to select private SNPs for each sample from a multisample VCF. Here is my workaround command:

java -Xmx16G -jar GenomeAnalysisTK.jar \ -T SelectVariants \ -R ${FASTA} \ -V ${VCF} \ -o ${SAMPLE}.snv.vcf \ -sn ${SAMPLE} \ --restrictAllelesTo BIALLELIC \ -select "AC==1" \ --keepOriginalAC
version: GenomeAnalysisTK-3.7-93-ge9d8068

However, the filtered private-SNPs output does not have private SNPs only. eg. AC_Orig is > 1 for most positions.
I'm wondering if there is something else I need to add or if you have any other suggestion to complete this task.

Many thanks,



  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Jose,

    The AC gives the number of alt alleles present in the genotypes, so by selecting AC==1, you are excluding hom var sites. Is that what you mean to do?

    Can you post some example records that are in your output VCF that should not be there?


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