Question: Split BAM by average coverage
gravatar for h.mon
4.6 years ago by
h.mon25k wrote:

I have a BAM file of a microbial genome assembly, performed on CLC (assembly+read mappings). The assembly has some contigs with extremelly low or high coverages - about ten-fold bellow or above the "average" average coverage. Is there a easy way to extract contigs based on average coverage thresholdds? I want to have a closer look and possibly reassemble those contigs.

For example, one contigs with much above average coverage seems to be rRNA genes, and there seems to be a lot of SNPs there. I want to reassemble these reads with more stringent settings and see if I have multiple copies of the rRNA genes.

bam assembly genome • 1.5k views
ADD COMMENTlink modified 4.6 years ago by Pierre Lindenbaum120k • written 4.6 years ago by h.mon25k
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

create a BED of your regions of interest and use, for example,  GATK DepthOfCoverage to get the mean depth of those regions.

Create a new BED file with the filtered regions

create a new BAM with 'samtools view -o new.bam -Lselect.bed old.bam'


ADD COMMENTlink written 4.6 years ago by Pierre Lindenbaum120k
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