remove reads that are mapped close each other

[wsuplantpathology]

Dear bazam team:

I have a quick question. Could you please write a script to remove the PE reads when the two reads in a pair are mapped within 1000 bp from a bam file? e.g.: if the mapping distance of the two reads in the pair is below 1000bp, then remove this pair from the bam file. Thanks so much.

Sincerely,
Chongjing

[ssadedin]

Hi @wsuplantpathology -

Bazam can do this by using the -f option to filter the reads. An example (which you might want to tweak) would be like this:

java -jar build/libs/bazam.jar  \
    -f '(pair.r1.referenceIndex == pair.r2.referenceIndex) && (Math.abs(pair.r1.alignmentStart-pair.r2.alignmentStar
t)>1000)' \
-bam test.bam > filtered.interleaved.fastq

Hope this helps and let me know if it doesn't make sense.

[wsuplantpathology]

Dear @ssadedin

Thanks so much for your quick response. For my understanding, your script was to keep the reads pairs that are mapped at distance above 1000 bp, am I right?

I think my situation is more complicated. Because my mapping has difference cases, please refer to this cartoon:

What I want to do is just discard the read pairs that are mapped within 1000 bp, and keep all read pairs in all other situations. I am looking forward to some suggestions. Thanks for your help, I really appreciate.

Sincerely,
Chongjing