somatic.sh

script for somatic SNP and Indel calling

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Last Update: 2024-05-27

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somatic.sh is a shell script to run varscan somatic for somatic variant-calling, and Annovar to annotate. It calls both SNPs and Indels. It also produces 2 MAF files compatible with MutSigCV.
Now the script allows for multithreading.
The script is updated according to new format.

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2017-07-30

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