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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Can I have multiple alleles in the ALT column? #50

Open carolynzy opened 5 months ago

carolynzy commented 5 months ago

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 commented 3 months ago

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

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!

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