Delly 1.1.3 CNV
- Coverage is too low!
error on germline A-mini and A-partial samples
#64
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Delly v1.1.3 issue in process
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For A-mini and A-partial samples, only chr8, chr21, and chrX were included but they should have enough "depths" for the specific regions. The error message probably indicated that Delly CNV failed because there's no coverage at all in chr1. (Increasing the window size wouldn't help as the whole chr1 don't have any reads) See https://confluence.mednet.ucla.edu/pages/viewpage.action?pageId=82391152 |
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Good news! output - So it looks like Delly v1.1.3 is now limited to select samples with good coverage for testing. This wasn't the case in Delly v1.0.3 or older version where CNV calling was possible on A-mini and A-partial samples. |
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Good news!
The process
call_gCNV_Delly
ran successfully and generated expected results for an A-full sample,CPCG0196-B1
.output -
/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.1.3/A-full-F72/call-gSV-4.0.0-rc.1/CPCG0196-B1/DELLY-1.1.3/output/DELLY-1.1.3_CNV_TEST_CPCG0196-B1.bcf
log -
/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.1.3/A-full-F72/delly1.1.3-A-full.log
So it looks like Delly v1.1.3 is now limited to select samples with good coverage for testing. This wasn't the case in Delly v1.0.3 or older version where CNV calling was possible on A-mini and A-partial samples.