Hi! I'm trying to merge a few VCFs that have been processed with HAT-FLEX. However, I'm getting the following error messages:
[E::bcf_calc_ac] Incorrect allele ("2") in SP0532850 at chr2:26477050
Upon closer look, it seems that HAT-FLEX created VCF lines with doubled up entries, where there's a semicolon-delimited ID field listing both variant IDs, but only a single ALT allele per row. In other words, HAT-FLEX is outputting each allele of a multiallelic site as a separate row, but copying the full dual INFO fields and full genotype from the original multiallelic record onto both rows.
Could you please assist? Thank you so much!
Hi! I'm trying to merge a few VCFs that have been processed with HAT-FLEX. However, I'm getting the following error messages:
[E::bcf_calc_ac] Incorrect allele ("2") in SP0532850 at chr2:26477050Upon closer look, it seems that HAT-FLEX created VCF lines with doubled up entries, where there's a semicolon-delimited ID field listing both variant IDs, but only a single ALT allele per row. In other words, HAT-FLEX is outputting each allele of a multiallelic site as a separate row, but copying the full dual INFO fields and full genotype from the original multiallelic record onto both rows.
Could you please assist? Thank you so much!