Hello,
I am looking for a way to mask positions below a certain coverage, i.e., convert all positions below x-fold coverage to N.
The problem is not calculating the coverage for each position (I can do that with BEDtools genomecov or BBmap pileup.sh), but the actual conversion of the input file. I was looking into BEDtools maskfasta for example, but couldn't find a way to set a specific coverage-threshold.
Thanks for any suggestion!
I am looking for a way to mask positions below a certain coverage, i.e., convert all positions below x-fold coverage to N.
The problem is not calculating the coverage for each position (I can do that with BEDtools genomecov or BBmap pileup.sh), but the actual conversion of the input file. I was looking into BEDtools maskfasta for example, but couldn't find a way to set a specific coverage-threshold.
Thanks for any suggestion!
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