Question: filters need to apply for Exome bam files after mapping
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gravatar for archie
11 months ago by
archie70
India
archie70 wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by archie70

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

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

ADD REPLYlink written 11 months ago by igor7.6k

Hi

Thank you for your suggestion.

ADD REPLYlink written 11 months ago by archie70
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