M2 pon created with GenomicsDB, skips germline, and reports stats #5675
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## master #5675 +/- ##
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- Coverage 87.043% 80.32% -6.723%
+ Complexity 31707 30118 -1589
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Files 1940 1940
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Branches 16130 16137 +7
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- Hits 127233 117496 -9737
- Misses 13051 23101 +10050
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| private static final double germlineProbability(final double alleleFrequency, final int altCount, final int totalCount) { | ||
| final double hetPrior = alleleFrequency * (1 - alleleFrequency) / 2; |
…nd reports frequency stats
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| * <h4>Step 2. Create a file ending with .args or .list extension with the paths to the VCFs from step 1, one per line.</h4> | ||
| * <p>This approach is optional. Other extensions will error the run. </p> | ||
| * <h4>Step 2. Create a GenomicsDB from the normal Mutect2 calls.</h4> | ||
| * Note that GenomicsDBImport is currently (as of February 2019) inefficient when processing multiple intervals. Therefore, |
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Depends on what your data looks like. For exomes it should be fine now if you use --merge-input-intervals #5540
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@ldgauthier The M2 pon wdl I wrote for this PR scatters over contigs, making a chr1 pon from a chr1 GenomicsDB, a chr2 pon from a chr2 GenomicsDB, and then merging. Are you saying that instead I should make a single GenomicsDB with --merge-input-intervals and create a single pon from that DB? Is this true even if it's a WGS pon and there are lots of variants?
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~24 contigs is probably not a big deal. (That arg also won't help WGS because each contig has to get its own interval anyway.) Exomes were the real pathological case because there's a very significant startup cost for each interval and even for scattered exomes we had O(1000) intervals.
| * --genomicsdb-workspace-path pon_db \ | ||
| * -V normal1.vcf.gz \ | ||
| * -V normal2.vcf.gz \ | ||
| * -V normal3.vcf.gz |
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you could also use a sample_map file if you have a lot of samples like Lee
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I would hope that anyone doing this on a large scale would be running via the WDL and wouldn't have to worry about an unwieldy command. But it can't hurt to mention, I suppose.
@takutosato This PR does a few things:
GenomicsDBimport in order to scale to more and larger inputs. This gets around problems that @LeeTL1220 encountered while making a REBC PoN from 250 noisy WGS samples.