Delly 1.1.3 CNV - Coverage is too low! error on germline A-mini and A-partial samples

[Faizal-Eeman]

Delly v1.1.3 issue in process call_gCNV_Delly:

This process fails with the following Command error.

for A-partial dataset

Command error:
  [2022-Aug-04 20:35:33] delly cnv --genome Homo_sapiens_assembly38.fasta --outfile DELLY-1.1.3_CNV_TEST_TWGSAPRT000001-T001-S01-F.bcf --svfile DELLY-1.1.3_SV_TEST_TWGSAPRT000001-T001-S01-F.bcf --mappability Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz BWA-MEM2-2.1_TEST0000000_TWGSAPRT000001-T001-S01-F.bam 
  [2022-Aug-04 20:36:03] Scanning Windows
  Please increase the window size. Coverage is too low!

The default scan-window parameter is 10,000. Tried increasing it to 100,000 and 1,000,000 but the command still gives the same error asking to increase the window size.

for A-mini dataset

Command error:
  [2022-Aug-04 22:06:30] delly cnv --scan-window 100000 --genome Homo_sapiens_assembly38.fasta --outfile DELLY-1.1.3_CNV_TEST_TWGSAMIN000001-T001-S01-F.bcf --svfile DELLY-1.1.3_SV_TEST_TWGSAMIN000001-T001-S01-F.bcf --mappability Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz BWA-MEM2-2.1_TEST0000000_TWGSAMIN000001-T001-S01-F.bam 
  [2022-Aug-04 22:06:45] Scanning Windows
  Please increase the window size. Coverage is too low!

This error is native to Delly v1.1.3 which suggests that the coverage is too low in the scanning window. This is due to the coverage check commit that has been newly implemented in Delly v1.1.3. Check out the code chunk that was added to this commit.

@pboutros and @tyamaguchi-ucla
Do we have coverage metrics for these test samples? I think this is because A-mini and A-partial datasets are downsampled version of A-full. I'd like to test this on one of the real samples that has a good coverage profile and see if the call_gCNV_Delly process of this pipeline goes through with this error.

Thoughts?

[tyamaguchi-ucla]

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

[Faizal-Eeman]

Assuming no coverage in regions other than chr8, chr21 and chrX, I tried to pass a target BED file to this command (--scan-regions) so that we focus only on these three chromosomes. Now the error message says Not enough windows!

Command error:
  [2022-Aug-05 00:41:14] delly cnv --scan-regions /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.1.3/config/targets-hg38.bed --genome Homo_sapiens_assembly38.fasta --outfile DELLY-1.1.3_CNV_TEST_TWGSAMIN000001-T002-S02-F.bcf --svfile DELLY-1.1.3_SV_TEST_TWGSAMIN000001-T002-S02-F.bcf --mappability Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz BWA-MEM2-2.1_TEST0000000_TWGSAMIN000001-T002-S02-F.bam 
  [2022-Aug-05 00:41:31] Scanning Windows
  Not enough windows!

The error message probably indicated that Delly CNV failed because there's no coverage at all in chr1

If there is no coverage in chr1, then the tool should still be able to proceed to other regions with coverage and call CNVs. This error actually stops Delly from moving ahead.

I'm still launching job to test this on an A-full dataset and get back on this.

[Faizal-Eeman]

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.