Selscan: ERROR: Alleles must be coded 0/1 only.

Question

[taniamahmood38]

I am trying to run nsl statistics using selscan tool on a vcf file (created using freebayes). But i am getting this error

ERROR: Alleles must be coded 0/1 only.

0 2

Kindly give me a solution because genotypes can be 2 3 so how to compute the statistics, in this case.

Many thanks in advance.

[Ram]

Please edit your post and add your freebayes command.

[taniamahmood38]

This was the freebayes command used to generate the vcf file..

  freebayes -f ref.fa aln.bam >var.vcf

Answer 1

[Pierre Lindenbaum]

you could filter out the multiallelic in the VCF using bcftools view -m2 M2 or convert multiallelic to biallelic using bcftools norm

[Ram]

Side note: Use vt decomp | vt norm instead of bcftools norm to retain information on the original variant entries after the operation. The added INFO/OLD_MULTIALLELIC field serves as a quasi-log of the operation.

[taniamahmood38]

Sure, I am grateful to you for helping me out thank you. I will try this out