Open soccin opened 5 years ago
Thanks @soccin - I switched from comma to semicolon in release v1.6.14
, but this looks like an unhandled exception when the input MAF uses commas, and is copied unchanged. I'll put a fix in the backlog, but let me know if you need a fix ASAP.
Not urgent. I have a local version I fixed for now. Thanks.
The VCF spec (https://github.com/samtools/hts-specs/blob/master/VCFv4.3.tex) says:
FILTER - filter status: PASS if this position has passed all filters, i.e. a call is made at this position. Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for filters that fail. e.g. “q10;s50”
Some VCF parsers are fussy about this; simple fix: