Comments (2)
I've just come across this same query, and, from what I can tell, genomecov
does use non-primary alignments. To figure this out, I compared it to calculations from mosdepth
.
# 1. bedtools genomecov
bedtools genomecov -bga -ibam input.bam > bedtools.depth.tsv
# 2. mosdepth defaults: excluding non-primary, QC fail, unmapped reads, and duplicates = bitwise flag 1796
mosdepth default input.bam
# 3. mosdepth: excluding QC fail, unmapped reads, and duplicates = bitwise flag 1540
mosdepth -F 1540 flag1540 input.bam
The results of (1) and (3) were identical.
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Thank you for doing the work I didn't!
Do you have any thoughts on the best way to exclude non-primary reads when running genomecov
?
Pre-filter with samtools view
?
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