filters need to apply for Exome bam files after mapping

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6.5 years ago

Omics data mining ▴ 260

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 • 1.3k views

ADD COMMENT • link 6.5 years ago by Omics data mining ▴ 260

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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 REPLY • link 6.5 years ago by igor 13k

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Hi

Thank you for your suggestion.

ADD REPLY • link 6.5 years ago by Omics data mining ▴ 260

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