- bump stream-vbyte for performance annotating
- fix #43 where output vcf would have Number=, unless number was specified in config.json
- skip non ACGT alts (@migbro #39)
- grab description from input vcf and propagate to annotated VCFs (@dmiller15, @migbro #34, #35)
- report missing float as . (thanks @dmiller15 #32)
- better help message indicating how to output bcf/vcf.gz (thanks @dvg-p4)
- fix missing value in cadd example (thanks @dvg-p4)
- doc types (thanks @enormandeau)
- handle big files (#30)
- add wiki page and more information about decomposing variants
- clarify warning on non ACGT (#23)
- better error messages on missing/bad zip file
- change VCF header (#19)
- output fewer warnings for '*' and other alternate alleles (#22)
- fix build on OSX (#18 from @sstadick)
- handle empty alts (#16 from @sstadick)
- add script for converting dbNSFP -> VCF -> echtvar encode
- fix bug with filter not removing (not filtering) variants correctly.
- exit with error on multi-allelics (previously, only first allele was used) ( #11)
- more docs on conf file (thanks @m-pauper)
- fix compression error for very dense regions (#12)
- fix error when using hts_set_threads more than once and after reading header (#12)
- fix #8. bug introduced for string values.
- support multiple echtvar files to
echtvar anno
. This makes it possible to annoate with, for example gnomad and dbsnp. - support string fields. This works for fields with a lowish number (max of thousands) of unique values.
- support extracting FILTER field from annotation VCF. So now can annotate with, e.g. gnomad FILTER field via:
in the json file for
{"field": "FILTER", "alias": "gnomad_filter"},
echtvar encode
. "FILTER" is a special-case, all otherfield
s are from the INFO.