Delly 1.1.3 vs older versions

[Faizal-Eeman]

Delly 1.1.3 was integrated in the call-gSV pipeline and evaluated for its CNV and SV calling on an A-full dataset, CPCG0196-B1.

For comparison on this A-full sample, results previously available from Delly 0.8.7 were compared with Delly 1.1.3. Overall, this version of Delly calls SVs/CNVs as expected while stringently calling variants in regions of acceptable/higher coverage. See Discussion #64 for limitations found in Delly 1.1.3 CNV calling.

Validation results directory - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.1.3/validation/A-full/

CNV Calling:

Only those CNV calls with FILTER=PASS (good quality CNVs) and FT=PASS (per-sample genotype filter), were considered for comparison of Delly 1.1.3 and Delly 0.8.7. Difference were observed in that,

• the CNV START and END coordinates were adjusted by a few base-pairs in Delly 1.1.3
• a few CNVs were novel to Delly 1.1.3

CNV results comparison file - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.1.3/validation/A-full/DELLY-0.8.7-vs-1.1.3-CNV-A-full.sdiff

SV Calling:

Only those SV calls with FILTER=PASS, FT=PASS and MAPQ>0 (Mapping Quality score > 0), were considered for comparison of Delly 1.1.3 and Delly 0.8.7. Difference were observed in that,

• the values such as # of high quality variant junction reads, etc., which are represented by the FORMAT column of the BCF file are slightly different in Delly 1.1.3
• Most SVs when considering the START and END coordinates appear to be similar between the two versions
• However, a few SVs called by v1.1.3 are not called by v0.8.7 and vice versa

SV comparison results - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.1.3/validation/A-full/DELLY-0.8.7-vs-1.1.3-SV-A-full.sdiff