I generated a multisample VCF file using GATK's HaplotypeCaller/GenotypeGCVFs method. 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?
(As a bonus, could a given solution take advantage of a list of chromosomes? Each "chromosome" (chr2, in the above example) is a pseudochromosome scaffold of contigs, and the genotype calls in the VCF refer to the contig names, not the pseudochromosome name. Each pseudochromosome consists of ~20 contigs.)
>less chr2.list ctg3 ctg78 ctg23 ctg746 ...