How to extract high coverage region from BAM?

Question

[BioGeek]

I want to extract ABNORMAL high coverage region from BAM or SAM files

'ABNORMAL high coverage' -- More than twice the size of average coverage

Answer 1

[Pierre Lindenbaum]

• 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 depth and awk (search biostars for this)