VarScan for tumor only files

Dear Group, I have tumor only targeted sequence amplicon data from MiSeq, I want to use VarScan to identify SNV and indels.

Can VarScan take tumor only BAM files? I dont have tumor-normal pairs!

Appreciate your input..

thanks Adrian

sequence alignment next-gen snp

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written 9.4 years ago by oriolebaltimore

Varscan you can use input as the mpileup file. Below is the command.

 /tool/Varscan/VarScan.v2.2.11.jar readcounts <mpileup> \
    --min-coverage 20 \
    --min-base-qual 30 \
    --output-file <output file name>

Hope this might be helpful to you.

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updated 9.4 years ago by Ram

• written 9.4 years ago by mks002

0 answers

No answers yet.

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