feat: filter manta calls #1371
feat: filter manta calls #1371
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Additional details and impacted files@@ Coverage Diff @@
## develop #1371 +/- ##
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+ Coverage 99.42% 99.44% +0.02%
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Files 41 39 -2
Lines 1916 1986 +70
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+ Hits 1905 1975 +70
Misses 11 11
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Let's use develop as the base branch. Maybe we'll include another PR or two for v14 :) |
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Looks good! The only thing is that I think it would be better if the manta filters were in a separate rule and not included in the manta rule. I understand this would mean more work though. Alternatively I wonder if the filtering step can be added to the svdb filtering, although that would potentially filter SVs from other tools too. But would be cleaner in my opinion
BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule
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Description
In here a number of different issues will be solved by a few small changes.
Relevant issues:
Added
Changed
Fixed
Removed
Documentation
Tests
Feature Tests
Verify correct Manta settings and filters
Manta setting
--exomeshould only be present in TGA casesSee TGA settings in screenshot below:
cleanfowl T only:
(exome argument set)
See WGS setting in screenshot below:
(no exome argument set)
Bcftools filter
low_pr_sr_countshould be correctly applied:See screenshot of example header from Manta T+N rule and Manta T-only rules below:
cleanfowl TGA T-only
case H WGS T-only
See example of applied filter in VCF example variant below in case sweetelf:
low_pr_sr_count
5 84761092 MantaINV:13082:1:2:0:1:0 C <INV> . low_pr_sr_count END=99239925;SVTYPE=INV;SVLEN=14478833;CIPOS=0,1;CIEND=-1,0;HOMLEN=1;HOMSEQ=A;INV3 PR:SR 774,1:2188,2PR:SR = 774,1:2188,2
Alt PR:SR = 1 + 2 = 3 smaller than 4 filter should be set!
PASS
22 37332762 MantaBND:23188:1:2:0:0:0:0 T T]10:35058943] . PASS SVTYPE=BND;MATEID=MantaBND:23188:1:2:0:0:0:1;CIPOS=0,6;HOMLEN=6;HOMSEQ=CAGGGA;BND_DEPTH=3401;MATE_BND_DEPTH=6 PR:SR 475,1:1146,4PR:SR = 475,1:1146,4
Alt PR:SR = 1 + 5 = 6 larger than 3 filter should not be set!
Validation status:
Validation of FLT3 detection in TGA cases
Criteria
In all downsampled HD829 cases tested the following criteria is met:
Results
First row is validation of V13.0.0
Bottom row is the results from this PR
As a side-note some of the above variants were not detected in Manta or DellySV previous to version 13.0.0, and were most likely rescued due to the inclusion of more informative reads for SV calling.
Sweetelf comparison of FLT3 detection in v13.0.0 and current PR.
Validation status:
Validation for detection of known SVs in WGS cases
Criteria
The following criteria need to be met:
Results
original case-ids hidden, find real case names here: https://docs.google.com/document/d/12x3ozQE62bk_yWNTBW_u8vZMqhpKFRMW3yizzM_mWZs/edit
Validation status:
Validation of detection of FLT3 in WGS cases
original case-ids hidden, find real case names here: https://docs.google.com/document/d/12x3ozQE62bk_yWNTBW_u8vZMqhpKFRMW3yizzM_mWZs/edit
This has not been previously tested in Balsamic, but WGS cases with known FLT3-ITD has been requested from cust110 and 4 WGS cases with known FLT3-ITD have been shared:
Out of these 4 shared cases however, only 1, H had a FLT3-ITD variant called by Manta, which will have to serve to investigate the effect of removing MaxDepth on WGS cases with FLT3-ITD.
Criteria
The following criteria need to be met:
Results
Validation status:
Pipeline Integrity Tests
.hkfile)Clinical Genomics Stockholm
Documentation
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Ensure that all checkboxes below are ticked before merging.
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conditions where applicable, with satisfactory results.