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mendelian2 plugin

Open biouserPD opened this issue 10 months ago • 1 comments

Hi, I am using mendelian2 bcftools plugin with this command :

bcftools +mendelian2 Input.vcf.gz --pfm 0705_WHOLE_BODY.CEL,F01_FOOT.CEL,M10_FOOT.CEL -m c

and I get this error: The sample is not present: M10_FOOT.CEL

but I'm sure the sample is present in the vcf file. if I move the order of the samples the last one in the list is always absent regardless of which one it is.
Any suggestions on how to fix this problem?

Thanks a lot

biouserPD avatar Mar 11 '25 13:03 biouserPD

Can you provide a small test case to reproduce the problem? Things you can check yourself:

  • which version of bcftools are you using? Does it fail also with the latest?
  • can you try bcftools view Input.vcf.gz -s 0705_WHOLE_BODY.CEL,F01_FOOT.CEL,M10_FOOT.CEL, just to make sure there really is no typo in the sample names?

pd3 avatar Mar 25 '25 19:03 pd3