Added liftover wdls and jsons for gnomAD 2.1 #5604
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Minor changes to test script.
Codecov Report
@@ Coverage Diff @@
## master #5604 +/- ##
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+ Coverage 87.035% 87.039% +0.004%
- Complexity 31535 31537 +2
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Files 1930 1930
Lines 145443 145443
Branches 16090 16090
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+ Hits 126586 126592 +6
+ Misses 12997 12992 -5
+ Partials 5860 5859 -1
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LeeTL1220
approved these changes
Jan 25, 2019
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@jonn-smith Minor point. Feel free to merge once addressed.
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| "LiftoverVcf.gatk_docker": "broadinstitute/gatk:4.0.11.0", | |||
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IS this something that general users would use? If not, maybe this should go into an unsupported directory? Especially, since I see some gs://broad-dsde-methods-jonn urls...
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Typically no.
As I mentioned in previous PRs, I have placed a file indicating that the data source scripts are unsupported in the data source scripts folder.
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| # Removes a given list of INFO field annotations from the given VCF files. | |||
| # | |||
| # Description of inputs: | |||
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Added WDLs to subset the INFO field annotations to only the allele frequency fields.
Also modified the
mutect2wdl to produce a gnomAD with only AF fields.@davidbenjamin - you may want to double-check my updates to the M2 support wdl.