Hi,
I would like to filter out or mask bases in my SAM file that has a quality value below a defined number. Is there a way to do this?
Alternatively I want to filter out the bases or mask them in my FASTQ file, but this has to be done without disturbing the BWA-MEM alignment, which I intend to do afterwards. This could possibly be done by replacing the law quality base call with a "N".
I am aware of quality trimming and removing reads by MAPQ, but this will not remove low quality bases within the read.
I would appreciate any input!
I would like to filter out or mask bases in my SAM file that has a quality value below a defined number. Is there a way to do this?
Alternatively I want to filter out the bases or mask them in my FASTQ file, but this has to be done without disturbing the BWA-MEM alignment, which I intend to do afterwards. This could possibly be done by replacing the law quality base call with a "N".
I am aware of quality trimming and removing reads by MAPQ, but this will not remove low quality bases within the read.
I would appreciate any input!
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