Mutect2 Option: --germline-resource

[maotian06]

Here is the benchmarking result of the newly added Mutect2 option --germline-resource:

Benchmarking

• Normal-paired-model :
  • sample: A-full-p2
  • vcf comparison result: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/vcf_comparsion_Afull.txt

Option	Total SNPs	Unique SNPs and %	Shared SNPs and %
With germline resource	133,585	10; 0.0%	133,575; 100.0%
W. O. germline resource	133,667	92; 0.1%	133,575; 99.9%

- sample: CPCG0196
- vcf comparison result: //hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/CPCG_vcf_comparsion_paired.txt

Option	Total SNPs	Unique SNPs and %	Shared SNPs and %
With germline resource	34,747	30; 0.1%	34717; 99%
W. O. germline resource	43,276	8559; 19.8%	34717; 80.2%

• Tumor-only-model :
  • sample: anaplastic thyroid cancer sample - MDA10
  • vcf comparison result: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/vcf_comparsion.txt

Option	Total SNPs	%Unique SNPs	%Shared SNPs
With germline resource	122,005	1488; 1.2%	120517; 98.8%
W. O. germline resource	3,552,165	3431648; 96.6%	120517; 3.4%

 - sample: CPCG0196
- vcf comparison result: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/CPCG_vcf_comparsion_tumor_only.txt

Option	Total SNPs	Unique SNPs and %	Shared SNPs and %
With germline resource	149,053	2737; 1.8%	146316; 98.2%
W. O. germline resource	189,592	3165672; 95.6%	146316; 4.4%

• Multiple-tumor-model :
  • sample:anaplastic thyroid cancer sample - ATCWGS21
  • vcf comparison result: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/vcf_comparsion_ATCWGS.txt

Option	Total SNPs	%Unique SNPs	%Shared SNPs
With germline resource	13,104	2; 0.0%	13,102; 100%
W. O. germline resource	13,561	459; 3.4%	13,102; 96.6%

• Comparison between tumor-only and paired Mutect2
  • sample: CPCG0196
  • vcf comparison result: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/CPCG_vcf_compare_paired_tumor_only.txt

Option	Total SNPs	%Unique SNPs	%Shared SNPs
Paired Normal-Tumor	34,747	14138;40.7%	20,609; 59.3%
Tumor-only	149,053	128,444; 86.2%	20,609; 13.8%

[maotian06]

The output files are stored here: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/4.0.0-rc.1/maotian-add-germline-resource/output/call-sSNV-3.0.0/