Extract the overlapping paired-end reads

Question

[ATRX]

Hi,

I would like to know if there is a way to extract paired-end reads (and the genomic region) from the bam file where a certain part of R1 and R2 read overlaps the genomic location. For example, if R1 and R2 are the paired-end read then, I am interested in extracting this paired-end read from the bam file and extract the region that is between **.

R1 -------**----------**>
     <----**----------**---- R2

Any advice or suggestions would be very helpful.

Thanks, -Ar

[lieven.sterck]

not directly what you ask for but you could first merge overlapping reads (eg with FLASH or BBMerge or such) and then map those and see where they map.

[ATRX]

Thanks! I will try it.

[Carlo Yague]

You can select overlapping mate pairs based on the template length (9th) field of SAM/BAM files. Quoting from How to quantify the overlapping reads in paired-end DNA sequencing to check the sequencing efficiency :

If the fragment length is less than the sum of two reads, it means your paired sequences are overlapped.

[GenoMax]

Can you not try samtools view region on the aligned BAM file to get the reads? Are you looking for consensus or the region from all read pairs?

[ATRX]

Yes, I am not interested in a particular region but the regions in the entire genome where the paired-end reads R1 and R2 overlaps.

[GenoMax]

In that case following @lieven's suggestion will allow you to pre-select reads that overlap. You could then take the merged reads and align them (or identify read headers that merged in the pre-aligned BAM file).