Bam file: replace low quality bases with "N"

Question

[Jautis]

Hello, is there any way to remove low quality score bases from bam files, leaving the space blank or replaced with a filler character (i.e. Ns)?

I have mapped my sequencing reads, and adjusted the base quality scores (using mapDamage, which is conceptually similar to GATK's BQSR). I would now like to remove bases that have quality score less than 20 prior to visualizing the misincorporation rate, regardless of what the read's mapping score was (understanding that there can be poorly called bases on a confidently mapped reads). Is there a tool to do this? Thanks in advance!

Answer 1

[Pierre Lindenbaum]

using samjdk: http://lindenb.github.io/jvarkit/SamJdk.html

 java -jar dist/samjdk.jar -e "final byte[] quals = record.getBaseQualities();final byte[] bases = record.getReadBases();if(quals==SAMRecord.NULL_QUALS || bases==SAMRecord.NULL_SEQUENCE) return record;for(int i=0;i< quals.length;i++) {if (htsjdk.samtools.util.SequenceUtil.isNoCall(bases[i]) || (int)quals[i]  >= 20) continue;bases[i]=(byte)'N';}record.setReadBases(bases);return record;"  in.bam

[Jautis]

Awesome, works like a charm. Thank you!