Hi,
I intend to compare the performance of Mutect2, Varscan2 and Somatic Sniper. The problem I observed is that compared to the first two variants callers, Somatic Sniper called very very few variants.
Here's how I run the command with Somatic Sniper: ~/INTERNSHIP/tools/somatic-sniper/build/bin/bam-somaticsniper -q 10 -G -L -F vcf -f ~/INTERNSHIP/data/GRCh38_full_analysis_set_plus_decoy_hla.fa ~/INTERNSHIP/data/SetB_M3_2.preprocessed.bam ~/INTERNSHIP/out/MRC5.preprocessed.bam ~/INTERNSHIP/out/somatic-sniper/nMRC5-tB3-2.somatic-sniperNOQ.vcf
I tried running it with and without the somatic quality option Q, which isn't present in Mutect2 and Varscan2, but it returned few variants yet again. For example, on the same files Mutect 2 returned 25039 variant while Somatic Sniper 827.
Here's the command I run with Mutect2: gatk --java-options "-Xmx16g" Mutect2 \ -R ~/INTERNSHIP/data/GRCh38_full_analysis_set_plus_decoy_hla.fa \ -I ~/INTERNSHIP/data/SetB_M3_2.preprocessed.bam \ -I ~/INTERNSHIP/out/MRC5.preprocessed.bam \ --normal MRC5 \ --tumor SetB_M3_2 \ -O ~/INTERNSHIP/out/mutect/nMRC5_tB3-2.mutect.vcf
Here's is the documentation of Somatic Sniper: https://github.com/genome/somatic-sniper/blob/master/gmt/documentation.md
Thank you in advance for any insight you might want to share.
