- add duphold annotations. (requires duphold v0.0.4)
- flip start and end for small percent of cases where that's a problem
- expose min sample weight to allow adjusting required support for each variant
- fix type in annotate (s/Number/Integer/)
- better error message in merge.
- use set -e in process calls so we don't exit with 0 even on failure
- don't use --sum in merge step. this reduces the size of CI when using
smoove merge
- add a
SHQ:smoove het-qualityscore to the FORMAT field and aMSHQ:mean smoove het-qualityscore to the INFO. Variants with a het-quality of 4 are quite good.
- sensitivity improvement by dropping reads with > 5 mismatches.
- sensitivity increases for variants without split reads.
- use a fixed length of 4 in merge (gives much better merging)
- add new annotate command which takes a gff and annotates with gene names
- increase max_reads argument to svtyper to reduce false negatives
- remove QCFail and duplicate reads from split and disc.bams. This is now
part of
smoovebut also fixed inlumpy_filterupstream.
- fix bug when using
-x/--removeprwith--genotype(thanks @brad for test-case)
- update command to match latest mosdepth
- bcftools and gsort are now required.
- output never goes to STDOUT
- output contigs to header
- add svtools to docker
- add option to remove PRPOS and PREND