If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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, Moderator admin

    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?


Sign In or Register to comment.