Variant-PostProcess (v3)

JUNO Version (2022-06-02)

Uses local SDIR/opt for old version of R (3.3.1); See opt.manifest for files if you need to recreate

This version does not work properly. But for now this is the best solution so currently being used in production.

This version fixes the problem with overlapping IN/DEL's in Haplotype VCF. It first fixes the Haplotype VCF and then uses the BIC post routines.

Name		Name	Last commit message	Last commit date
Latest commit History 213 Commits
FixMultiInDel @ 4378ed1		FixMultiInDel @ 4378ed1
facets-suite @ 41a01fe		facets-suite @ 41a01fe
misc		misc
testing		testing
wes-filters @ 6fe5540		wes-filters @ 6fe5540
.gitignore		.gitignore
.gitmodules		.gitmodules
README.md		README.md
_MAF_HEADER		_MAF_HEADER
bSync		bSync
deliverResults.sh		deliverResults.sh
doPostProcessV3.sh		doPostProcessV3.sh
filterMAF.sh		filterMAF.sh
getMergedMAF.sh		getMergedMAF.sh
opt.manifest		opt.manifest
reRunHaplotect.sh		reRunHaplotect.sh
report01_v2.R		report01_v2.R
vcf2MultiMAF_b37.sh		vcf2MultiMAF_b37.sh