Merge paired end reads after mapping in BAM files

Question

[muhammad_elhossary]

Dear Experts, For some special application, I want to merge the read pairs of paired end reads from a BAM file, including the discordant reads, given that the genomic location is already known from the mapping to reference genome. I would mainly consider the following two conditions:

1- overlapping reads

1      7
=======>
    ||||
    <=========
     4      10

That would give me one read, like this.

1          10
============>

2- discordant reads.

Ref==============================================
         5          10^^^^^^^^^
         =====R1=====>|||||||||
                      |||||||||
                               <=====R2======
                               15          20

This one would result in:

        ================================>    
         5                             20

So, in other words, I want to reconstruct the missing fragment in the discordant pairs.

Are there any tools that can do that? Best wishes

[GenoMax]

For case #1 you can use tools like bbmerge.sh, FLASH, PEAR etc before you align the data. If the reads overlap then they will merge. No need for alignment. bbmerge.sh can trim off adapters etc.

For #2 you can take a look at samtools consensus (LINK). I don't think it will generate a single read for every pair like you seem to want.

[rfran010]

I might be missing something but situation 2 is not a discordant pair? But seems like a proper/normal pair that do not overlap.

That said, I expect bedtools can help you, https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html