Question: filters need to apply for Exome bam files after mapping
0
gravatar for archie
2.0 years ago by
archie90
India
archie90 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 2.0 years ago • written 2.0 years ago by archie90

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 2.0 years ago by igor10k

Hi

Thank you for your suggestion.

ADD REPLYlink written 2.0 years ago by archie90
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