Delly 1.0.3 vs older versions

[Faizal-Eeman]

Delly 1.0.3 was integrated in the call-gSV pipeline and evaluated for its CNV and SV calling performance on A-mini and A-partial datasets.

Validation results directory - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/

A-mini dataset:

No difference in CNV and SV calling results were found between Delly 1.0.3 and Delly 0.9.1.

CNV results - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/A-mini-F16/delly-0.9.1-vs-1.0.3_CNV.sha512
SV results - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/A-mini-F16/delly-0.9.1-vs-1.0.3_SV.sha512

A-partial dataset:

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 1.0.3 and Delly 0.8.7. No significant difference between the results of the two versions except for two CNV calls that appear to be novel to Delly 1.0.3. These two CNV calls are homozygous deletion events but do not seem to be variants of critical interest because of reasons below,

• chr21:9729136-9908431 - Intergenic CNV event with Read Depth based Copy Number of 0 suggesting close to no coverage in this genomic region. A visual of this genomic region from UCSC genome browser (hg38).
• chrX:95795851-95796482 - A 631 bp intergenic CNV event with Read Depth based Copy Number of 0 suggesting close to no coverage in this genomic region. A visual of this genomic region.

Comparison results are here - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/A-partial-F32/DELLY-0.8.7-vs-1.0.3-CNV-PASSED.sdiff

SV calling:

Only those SV calls with FILTER=PASS and MAPQ>0 (Mapping Quality score > 0), were considered for comparison of Delly 1.0.3 and Delly 0.8.7.

Delly 0.8.7 SV results - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/A-partial-F32/DELLY-0.8.7-SV-Only-PASS-and-MAPQ-gt-zero.txt
Delly 1.0.3 SV results - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/A-partial-F32/DELLY-1.0.3-SV-Only-PASS-and-MAPQ-gt-zero.txt

Differences are observed between the two versions,

• A few SVs called by v1.0.3 are not called by v0.8.7 and vice versa. Some of these SVs appear to be in the intergenic regions of the genome.
• v1.0.3 generally appears to give a higher number of SV calls
• Comparison results - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-update-delly-0.9.1-to-1.0.3/validation_delly0.9.1-vs-1.0.3/A-partial-F32/DELLY-0.8.7-vs-1.0.3-SV-PASSED.sdiff