Get discordant read pairs from bam

Question

[paulaotero.sanchez]

Hi,

I would like to know if there is a way to isolate discordant read pairs from a bam file. For example, when I use samtools stats in my bams, I can see the number of outward oriented read pairs and I would like to work just with them, is there a way to do that with samtools?

Thanks

[Pierre Lindenbaum]

Identifying discordantly mapped reads

Answer 1

[benformatics]

I found using samflags can get a bit confusing depending on the specific aligner-added flags and downstream BAM processing (i.e. marking duplicates).

https://github.com/GregoryFaust/samblaster has worked well for me in the past