Can I have multiple alleles in the ALT column?

[carolynzy]

Hi, thanks for developing this useful software!

I have a problem about the input file. I have a vcf file containing 420 samples with a reference genome of ~400m bps. For some loci, different samples may have different alleles, e.g., "C,T" in the ALT column. I found that these loci were filtered out in the HeaderCheckFailed category.

If I'm confident in these alleles, is it possbile to include these loci? Or maybe I'm doing something wrong? I really appreciate your help. Thank you!

[alachins]

Hi This is not supported in RAiSD. Best regards, Nikos

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On Wed, Apr 3, 2024 at 4:38 AM carolynzy ***@***.***> wrote: Hi, thanks for developing this useful software! I have a problem about the input file. I have a vcf file containing 420 samples with a reference genome of ~400m bps. For some loci, different samples may have different alleles, e.g., "C,T" in the ALT column. I found that these loci were filtered out in the HeaderCheckFailed category. If I'm confident in these alleles, is it possbile to include these loci? Or maybe I'm doing something wrong? I really appreciate your help. Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis