Missing PASS in SNP file

schatzlab / crossstitch

Code for phasing SVs with SNPs

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Missing PASS in SNP file #5

Open fritzsedlazeck opened 5 years ago

fritzsedlazeck commented 5 years ago

I would suggest to maybe put in a warning or error if there are no SNPs after filtering. We just spent some time to debug an issue and it came down to that the SNP caller did not specify PASS variants.

Thanks Fritz