How to extract high coverage region from BAM?
I want to extract ABNORMAL high coverage region from BAM or SAM files
'ABNORMAL high coverage' -- More than twice the size of average coverage
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Pierre Lindenbaum
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BioGeek
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BioGeek
1 answer
- get the mean coverage with gatk: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php
- get the positions having a depth > 'x' with
samtools depthandawk(search biostars for this)
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