search

mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
http://advntr.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
41 stars 15 forks source link

vcf header #38

Closed psychrb closed 3 years ago

psychrb commented 3 years ago

In trying to merge adVNTR output files across multiple samples using bcftools merge, I get an error: [W::vcf_parse] FILTER ' .' is not defined in the header [E::vcf_parse] Could not add dummy header for FILTER ' .'

1) Is FILTER " ." not meant to be included...No FILTER "PASS" in my output...Only "." 2) Should I just edit vcf file header to add ##FILTER=<ID=., Description="xyzzy"

FILTER=

3) Would you suggest an alternative way to merge files across samples? Other than bcftools..?

psychrb commented 3 years ago

To simplify, please disregard, as it seems these calls with FILTER "." did not PASS...And should be filtered out/excluded.