Add a cli option to keep filtered variants in the output VCF file with the FILTER attribute indicating why the variant was dropped.
Additional Functions
Explain the signature and output of a new API function, in a similar style to
that of Julia docstrings.
Additional Arguments
--keep-filtered, -k
Keep filtered variants in the output VCF file
Additional Output
The output VCF file should include ALL variants that were found in the BAM file, but if they didn't pass, they should be marked with the appropriate FILTER attribute. The attributes are
This would be a nice troubleshooting feature for both code and sequencing, and might indicate which parameters need to be tweaked if known variants aren't being called.
MillironX
commented
1 year ago
Add a cli option to keep filtered variants in the output VCF file with the
FILTERattribute indicating why the variant was dropped.Additional Functions
Explain the signature and output of a new API function, in a similar style to that of Julia docstrings.
Additional Arguments
--keep-filtered, -kAdditional Output
The output VCF file should include ALL variants that were found in the BAM file, but if they didn't pass, they should be marked with the appropriate
FILTERattribute. The attributes arehttps://github.com/ksumngs/HapLink.jl/blob/1a20311b949efb756cdfd5fd18463fd4302df74e/src/variantcalling.jl#L116-L123
Context
This would be a nice troubleshooting feature for both code and sequencing, and might indicate which parameters need to be tweaked if known variants aren't being called.