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New variant calling tools need WDL tasks #119

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5 tasks done
mark-welsh opened this issue Sep 20, 2019 · 0 comments
Open
5 tasks done

New variant calling tools need WDL tasks #119

mark-welsh opened this issue Sep 20, 2019 · 0 comments
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mark-welsh commented Sep 20, 2019 •
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Will be adding:

  • Strelka2, an Illumina tool for somatic SNV/Indel calls; tumor normal compatible
  • Manta, another Illumina tool for SV calls
  • Control-FREEC, for CNVs (this is has an interesting runtime setup)
  • MuTect2 (GATK4)
  • LoFreq
@mark-welsh mark-welsh self-assigned this Sep 20, 2019
mark-welsh added a commit that referenced this issue Sep 20, 2019
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[refs #119] Adds tasks for LoFreq, MuTect2, Strelka2
635086f 
these already existed in the DGD/nbl repo
mark-welsh added a commit that referenced this issue Sep 20, 2019
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[refs #119] Adds task for Manta
50f8e7f
mark-welsh added a commit that referenced this issue Sep 20, 2019
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[refs #119] Makes normal optional; var name change
1dafd27 
removed naming with "bam" since CRAM can also be input to this tool
mark-welsh added a commit that referenced this issue Sep 20, 2019
@mark-welsh
[refs #119] Adds first draft of Control-FREEC
2a9aa48 
need to run it to figure out the output files...
mark-welsh added a commit that referenced this issue Sep 23, 2019
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[refs #119] Adds missing var; corrects read orientation
56f5a36
mark-welsh added a commit that referenced this issue Sep 23, 2019
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[refs #119] orientation back to 0
65386f1 
this should be the case, in WGS pipeline the bam is sorted on-the-fly
via pipes and sambamba
mark-welsh added a commit that referenced this issue Sep 23, 2019
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[refs #119] Changes Boolean to String
c73a055 
variable is used in the bash routine so it does not need the WDL type
mark-welsh added a commit that referenced this issue Sep 24, 2019
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[refs #119] Made BED optional in LoFreq
438ca52
mark-welsh added a commit that referenced this issue Sep 24, 2019
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[refs #119] Changes orientation to FR and sorts
3311a15 
sambamba and samtools need to be turned on
mark-welsh added a commit that referenced this issue Sep 24, 2019
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[refs #119] Adds Control-FREEC output
e46574c
mark-welsh added a commit that referenced this issue Sep 24, 2019
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[refs #119] "intervals" needed conversion to String
32f555e 
because this is technically optional, like in the case of WGS, specifing
no intervals causes the command to fail. now it is converted to a String
array so even when its empty, the command populates with empty strings
and the cmd succeeds
mark-welsh added a commit that referenced this issue Sep 24, 2019
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[refs #119] Fixes Mutect (not MuTect!) typo
dd5736f
mark-welsh added a commit that referenced this issue Sep 24, 2019
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[refs #119] Removes dbSNP/COSMIC options
1fcefa3 
these aren't supported in GATK4/Mutect2, they should all be provided as
"germline resources"
mark-welsh added a commit that referenced this issue Sep 27, 2019
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[refs #119] Fixes typo that caused Cromwell to fail
a2c8149 
S -> s so that Cromwell can find the file
mark-welsh added a commit that referenced this issue Oct 2, 2019
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[refs #119] Doubles LoFreq memory
6df8a20 
12 GB was not enough for large (WGS) bams 🤷‍♂️
mark-welsh added a commit that referenced this issue Oct 14, 2019
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[refs #119] Moving manta to a generic branch
6e52734 
see #125
mark-welsh added a commit that referenced this issue Oct 17, 2019
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[refs #119] ControlFREEC now compatible with WES
5efabf1
mark-welsh added a commit that referenced this issue Jan 4, 2020
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[refs #119] grabs the VCF idx for output
5d7af52
mark-welsh added a commit that referenced this issue Jan 6, 2020
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[refs #119] Adds sample_id to Strelk2 for named output
543deff
mark-welsh added a commit that referenced this issue Jan 6, 2020
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[refs #119] Output file from cmd now matches
e7afedd
mark-welsh added a commit that referenced this issue Jan 7, 2020
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[refs #119] Adds GATK v3.8 of MuTect2
2a2004a
mark-welsh added a commit that referenced this issue Jan 7, 2020
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[refs #119] No newline char in command stanza
b8e9413
mark-welsh added a commit that referenced this issue Jan 8, 2020
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[refs #119] Add cosmic and dbsnp in lieu of germline
ae04c0a
mark-welsh added a commit that referenced this issue Jan 8, 2020
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[refs #119] Adds -nct to MuTect2
05170eb
mark-welsh added a commit that referenced this issue Jan 8, 2020
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[refs #119] Adds F1R2 output to GATK4 MuTect2
9df96e7 
important for FFPE tumor samples, see "Learn Orientation Bias Artifacts":
https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels-
mark-welsh added a commit that referenced this issue Jan 8, 2020
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[refs #119] GATK4 MuTect2 sets java mem explicity
0ebba1a
mark-welsh added a commit that referenced this issue Jan 12, 2020
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[refs #119] Adds panel of normals index
6a4b776
mark-welsh added a commit that referenced this issue Feb 8, 2020
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[refs #119] Outputs MuTect2 stats
dce275e 
This is needed by FilterMutectCalls
mark-welsh added a commit that referenced this issue Nov 12, 2020
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[refs #119] Separate task for strelka2 snvs+indels
f1d096c 
GATK now required
mark-welsh added a commit that referenced this issue Nov 13, 2020
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[refs #119] fixing dictionary typo
c4735e7
mark-welsh added a commit that referenced this issue Nov 13, 2020
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[refs #119] Always replace TUMOR, replace NORMAL if provided
630c3af
mark-welsh added a commit that referenced this issue Nov 13, 2020
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[refs #119] More sophisticated sed cmd (w/ gzip)
3b8dc84
mark-welsh added a commit that referenced this issue Nov 14, 2020
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[refs #119] MergeVcfs does not output .gz, so skip all that nonsense
70f010a
mark-welsh added a commit that referenced this issue Nov 16, 2020
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[refs #119] bash syntax bug fix
18b52dd
mark-welsh added a commit that referenced this issue Nov 16, 2020
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[refs #119] Strelka2 does not output gzip'd VCFs
cb8a473
mark-welsh added a commit that referenced this issue Nov 16, 2020
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[refs #119] -z tests for emptiness, we need not empty
d7b6e17
mark-welsh added a commit that referenced this issue Nov 16, 2020
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[refs #119] Again, no .gz VCF
58e5f1a
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