parent 2b9af68
author Mark Walker <[email protected]> 1701883462 -0500
committer Mark Walker <[email protected]> 1718121961 -0400

parent ceb41fc
author Mark Walker <[email protected]> 1701883462 -0500
committer Mark Walker <[email protected]> 1715005950 -0400

parent 9ad640d
author Mark Walker <[email protected]> 1701883462 -0500
committer Mark Walker <[email protected]> 1704486807 -0500

Add scramble filter

Realignment

Add bwa to mini docker

Build bwa from git

Use /opt/bin

Start in /opt

Runtime parameters

Fix alignment command

bump memory

Make scramble vcf python script

Scramble make vcf task added

Fix realignment bai path

Missing sv_pipeline_docker input

Fix scramble table output

Buffered clustering

Fix reverses

Use samtools view -M; realign from Scramble table instead of vcf

Fix interval generation and only realign soft-clipped reads

Slop 1 base

Slop 150 bases

And merge

Change scramble priority in overlap bp filter; update dockers

Reduce realignment cores to 4

Sort scramble table

Fix wdl

Update json templates

Bump realignment memory to 12gb

Update script to filter on indels

Indel filtering switch

Update

Add MEI intervals and manta/wham filtering

Delete comments

Optimize mei tree loading; consume table directly

Add scramble_min_clipped_reads

Fix reads_index_

Update scramble vcf script args

Add missing vcf script input in GatherSampleEvidence

LINE1 to L1 alt

Give preference to MEI over Manta insertions in breakpoint overlap filter

Update dockers with last build

Update dockers

Reduce memory usage in RealignSoftClippedReads

Bump realignment memory

Add manta_vcf_input in case manta isn't run but scramble is

Increase min_clipped_reads to 5

Bump memory

Update scramble commit

Bump MakeScrambleVcf memory to 4

Reduce min reads to 3

Add mei tree padding and alignment_score_cutoff

Select alignment score cutoff based on aligner

Update dockers

Remove debugging lines

Add scramble_mei_bed

Add scramble_mei_bed to test template

Bump ScramblePart1 to 3 GB

Adjust scramble clipped reads threshold based on coverage

Top level scramble_min_clipped_reads_fraction optional

Update dockers

Add mw_scramble_filter to ResolveComplexVariants in dockstore.yml

Update dockers

Update dockstore yml

Final touches

Update templates; add SVA filter

Revert unnecessary changes

Lint

Update readme

Update single sample pipeline and gathersampleevidence batch

Update readme

Readme grammar

Scramble intermedates description in README

Add comments to scramble vcf script

Minor fix