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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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filter -f germline #391

Open thedam opened 3 weeks ago

thedam commented 3 weeks ago

hey, How does this filter work?

delly filter -f germline -o germline.bcf merged.bcf What criteria it uses?

With some set of samples I get no output, so I wonder if I could write my own filter directly on the output files from this command: delly call -g $ref38 -x $dellyexc $bam -o ${sname}.bcf

Cheers

tobiasrausch commented 3 weeks ago

The germline filter compares SV carriers with SV non-carriers for various parameters (such as read-depth or paired-end support) to distinguish likely false positive and likely true positive germline SVs. This works better with increasing numbers of samples (definitely >25).