filters need to apply for Exome bam files after mapping

Question

[Omics data mining]

Hello everyone

I have exome sequence data of cancer patients. I did quality filtration and mapping using bowtie2. What are filteration of bam files required for the downstream analysis . Should I go with uniquely mapped or multi mapped reads ?? (As many of samples, percentage of uniquely mapped reads is < 20 %). ??? My goal is to predict the CNVs and SNPs by using GATK.

All suggestions will be appreciated

Thank you Archana

[igor]

My goal is to predict the CNVs and SNPs by using GATK

Why not follow GATK recommendations? https://software.broadinstitute.org/gatk/best-practices/

[Omics data mining]

Hi

Thank you for your suggestion.