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compute normal-tumor coverage ratio from exome BAMs

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.

(normal_unique_mapped_reads/tumor_unique_mapped_reads).

java -jar VarScan.jar copynumber normal-tumor.mpileup
output.basename -min-coverage 10 --data-ratio
[data_ratio] --min-segment-size 20
--max-segment-size 100

varscan gatk exome samtools bedtools
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updated by Chirag Nepal Chirag Nepal • written by tayebwajb tayebwajb

1 answer

Hi tayebwajb,

Did you manage how to extract the uniquely mapping reads from normal-tumor.mpileup or from bam files.

thanks !

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written by Chirag Nepal Chirag Nepal

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