Open JosephLalli opened 1 year ago
Hello, a similar question here. Is it possible to force shapeit not to impute missing variants?
To clarify, I underestimate that imputation is a necessary part of the phasing process. I think it would be helpful if the SHAPEIT team provided one small feature, and some guidance:
1) A FORMAT tag to indicate when a missing allele has been imputed (ideally with some sort of imputation quality metric, but I understand that would be difficult if such a metric isn't already being measured internally)
2) A recommended method of handling sites when one allele is in an already represented deletion. This is often encountered when one allele is a structural variant. If there is no recommended method, in general how would you recommend we use shapeit to phase structural variants?
Hello,
As an experiment, I've tried take the vcf of the draft human pangenome, use bcftools +setGT to unphase the pangenome vcf, and then rephase the vcf using different reference panels. I am using shapeit5's switch tool to assess phasing accuracy. I am using the re-phased dataset as estimated vcf, and the original pangenome vcf as the verification vcf. The advantage of this method is the elimination of genotyping as a source of error, as the input vcf was generated from the verification vcf.
Switch, however, is detecting sporatic genotyping errors. These errors are occurring at sites with a ./1 genotype.
Variants with a combined indel/snp, like so:
After using bcftools norm to split multiallelic sites, the pangenome VCF represents this region as: chr1 2 ATTGTCT A 1|0 chr1 4 T C .|1
Shapeit seems to be interpreting the .|1 call as a missing allele, and imputing the genotype at the site as 0/0. I don't think that is functioning as intented.
What is the best way to handle sites like this? If I used the atomize option of bcftools norm, I could represent the deletion allele as "*". Would shapeit recognize this?
Thanks!