Somatic variant calling for unpaired samples

01 January 1970 1 4K Report

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.

Snijesh V.P.

The pipeline explianed in gdc portal also deals with tumor only mode variant calling

https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

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