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Selectively eliminating a set of chromosomes per sample in a multisample VCF

mmats010mmats010 Riverside CAMember
edited April 2017 in Ask the GATK team

Hello,
In my multisample VCF file, some samples have aneuploid chromosome numbers. For example, Sample1 might be 2N for chr1, chr2, and chr3. Sample2, however, might be 2N for chr1 and chr3, but 3N for chr2.

Is there a way to selectively exclude all of the sample genotypes for Sample2/chr2, while leaving all other sample genotypes for chr2 (and all other chromosomes for Sample2) intact?

I already tried removing the individual chromosomes in the sample .g.vcf files using vcftools and the "--not-chr" options, then re-running GenotypeGVCFs. However, this still included calls for the excluded chromosomes for all of the specified samples, and I can't figure out where the calls themselves were originating from.

Perhaps there is a way to set sample genotypes to "NoCall" for individual chromosomes?

Thanks,
Mike

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