annotate a VCF with other VCFs/BEDs/tabixed files
This fixes a major bug in v0.3.4 (#150). Please update.
Full Changelog: https://github.com/brentp/vcfanno/compare/v0.3.4...v0.3.5
This release fixes and issue where the FORMAT column was added to the VCF header when no samples were present.
Full Changelog: https://github.com/brentp/vcfanno/compare/v0.3.3...v0.3.4
This contains minor usability fixes.
this release has minor fixes to by_alt and other bugs:
this release adds support for CSI. this can greatly speed up dense files like CADD and even gnomAD or ExAC.
to use, simply index your file with tabix as, e.g.:
tabix -m 12 --csi $file
and vcfanno
will prefer the .csi index over the .tbi.
refer to the performance page for how to optimize. in brief, setting
export IRELATE_MAX_GAP=1000
seems to give good results. Please experiment and let me know what works for you. I can get ~60% speed improvement using csi'd ExAC to annotate clinvar with the above changes.
setid
builtin to set the ID field and remove need for lua and fix some bugs.self
with multiple alternates when there were multiple overlaps (thanks Matthew).by_alt
that will have Number=A and will append multiple annotations for the same alternate
(from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333
when the 1st alternate has a single value and the 2nd alternate has 2 values.setid
builtin to set the ID field and remove need for lua and fix some bugs.self
with multiple alternates when there were multiple overlaps (thanks Matthew).op
by_alt that will have Number=A and will append multiple annotations for the same alternate
(from the same file) and output them as pipe-delimited. e.g with 2 alts, it might look like: 0.111,0.222|0.333
when the 1st alternate has a single value and the 2nd alternate has 2 values.