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kylessmith / SomVarIUS

Somatic variant identification from unpaired samples
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How to use for Somatic Mutation determination. #3

Open vivekruhela opened 6 years ago

vivekruhela commented 6 years ago

I am sorry, if I am asking too simple question but after reading read-me file, I am bit confused by the term unpaired data because I am using pair-end data in fastq file and finally after completion of my pipeline, I have annotation output from ANNOVAR along with vcf file. So how can use SomVarIUS for somatic mutation determination. Thanks.

pamonlan commented 4 years ago

With unpaired data, it is referred to as Tumor/Normal data. You can use pair-end reads from the sequencing of tumor sample and use somvarius to call al somatic variants. If you have normal and tumor data you can use another variant calling like Mutect2, VarScan, Octopus, etc.