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tpbilton / GUSMap

Genotyping Uncertainty with Sequencing data and linkage MAPping
GNU General Public License v3.0
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Error in VCFtoRA #16

Closed GGFHF closed 4 years ago

GGFHF commented 5 years ago

Dear Dr. Bilton

I I am trying to use VCFtoRA function on my vcf files, and I get an error requesting AD, RO o AO fields. I used bcftools for variant calling and my vcf files don't have those fields. However, they do have DP4 field, and in the help of the function you say that it can handle that information, although there is no argument to "coerce" VCFtoRA to search for the DP4 field. My files contain multiple samples that were merged with vcftools. Could here be the issue?

Congratulations for your work and thanks in advance,

Unai

tpbilton commented 5 years ago

Hi Unai,

The current version should handle DP4 information. I have gone through the function and checked for any problems but am able to get it to work.

VCFtoRA does require that "DP4" appears in the FORMAT field of the VCF for every SNP. If that is not the case, then it will fail (maybe there is a SNP or two in your VCF file where the DP4 information is missing for some reason?). I have updated the error messages and it should now tell you which SNP it stops at.

I'd suggest checking your VCF file and if the DP4 is there. If it is, could you show me a subset of your VCF and I might be able to see what is causing the problems.

Hope this helps.

Thanks, Timothy