VarScan for tumor only files

Question

[oriolebaltimore]

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

[mks002]

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.