filters need to apply for Exome bam files after mapping · Biostar

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filters need to apply for Exome bam files after mapping

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

exome alignment sequencing collecthsmetrices

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written 8.2 years ago by Omics data mining

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

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

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written 8.2 years ago by igor

Hi

Thank you for your suggestion.

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written 8.2 years ago by Omics data mining

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