Entering edit mode
8.9 years ago
tayebwajb ▴ 120
Could someone please suggest a quick way to compute the data ratio of uniquely mapped reads in
the normal to uniquely mapped reads in the tumor, as required by Varscan in the command below? I have over 50 exome BAMs.
java -jar VarScan.jar copynumber normal-tumor.mpileup
output.basename -min-coverage 10 --data-ratio
[data_ratio] --min-segment-size 20