Laura Gauthier

ReblockGVCF bug: first position on contig missing

2

## Bug Report ### Affected tool(s) or class(es) ReblockGVCF ### Affected version(s) - [x] Latest public release version [4.2.6.1] - [x] Latest master branch (probably) ### Description First position on...

GenotypeGVCFs can't handle somatic GVCFs from DRAGEN 3.8.4

1

## Bug Report ### Affected tool(s) or class(es) GenotypeGVCFs ### Affected version(s) - [x] Latest public release version [version?] - [x] Latest master branch as of [date of test?] ###...

Subsetting for A-length annotations (e.g. AF, PRI, F1R2, F2R1),

9

accounting for incorrect input lengths

GenomicsDB excessive logging "[E::faidx_adjust_position] The sequence "chrX" was not found"

3

## Bug Report ### Affected tool(s) or class(es) GenomicsDBImport ### Affected version(s) - [ ] Latest public release version [version?] - [x] Latest master branch as of Apr 4, 2022...

Add annotation checks to ValidateVariants

2

Ideally for GnarlyGenotyper inputs and outputs, check to make sure required Gnarly annotations are present, AS annotation lengths are correct, necessary VQSR annotations are present.