Subset BAM file based on selected coverage, PacBio reads
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3.4 years ago
MyrNat • 0

Hi, I have a Canu assembly (Pacbio reads). I want to use arrow to polish my assembly but beforehand I want to subset my raw reads to have a coverage of around 80X. The output from pacbio was a single subreads.bam file with coverage of 150X. I read that polishing coverage above 100X does not really improve the quality, so I want to test different coverage values. My question is how to create a new BAM file from the original that has e.g 80X coverage and is compatible with pbalign/blasr. I found several posts saying that using samtools is not going to work as the BAM generated file does not contain all the info needed by blasr. Thanks, Myrsini

pacbio arrow coverage BAM pbalign • 922 views
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