somatic variant calling

Question

[nikitanaik224]

I am looking for tools/methods for somatic variant calling for unpaired samples. The somatic variant calling through GATK best practices is specifically for tumor/normal paired samples. My study entails somatic variant analysis studying complex disorders, thus I have unpaired samples. I found following options: Samtools, ISOWN, Mutect (only tumor mode) and SomVarIUS . I would like to compile as many options as i could and choose the best suitable for my study. Kindly suggest further options and any opinions and suggestions are welcome.

[igor]

Check this previous discussion: single sample somatic variant calling software

Answer 1

[2nelly]

I don't think you will find something more advanced than GATK's Mutect. Since, you don't have matched normal samples, you can use a panel of normals. If I am not mistaken GATK team provides panel of normals. Of course you can prepare it by yourself using publicly available data. I also recommend to filter out variants using dbSNP common variants.