Adding an ancestral (ANC) individual to a vcf file
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21 months ago
hemr3 • 0

I'm working with the programme admixfrog to show lines of introgression into specific lineages. To do this, I need to adapt my VCFs so they have an 'ANC' or ancestral individual that ALWAYS carries the ancestral allele, and then whether this matches the reference.

if the ANC individual doesn't have the same allele as the reference on the ANC column it should say 1|1. if the ANC individual matches the reference the ANC column should say 0|0 if the ANC individual and all samples match, the ANC column should say 2|2 if there is no data (as is often the case with aDNA) the column should say .|.

I have a programme (handwritten) on python that does produce the VCF files that I need, BUT the issue arises when I try to use it alongside the admixfrog algorithm - i get the error on Linux terminal: NotImplementedError: seek not implemented in files compressed by method 1.

What could be causing this? I don't want to touch the admixfrog code to try and inject an older version of pysam, which might work, but also might render the programme useless. If there's a tool that I could use to side-step using the programme I'm currently using to see if that solves the issue, that'd be great!


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