Structural Variation; Discordant Pairs?

Question

[Rm]

For structural variation (SV) study: Following hydra or SVdetect or other pipelines;

I Need some clarification on type(s) of discordant reads from a mate pair or paired end analysis to be retained as inputs for the above programs.

We remove concordant reads (both forward and reverse reads aligned within the permisible range (depends on insert size) to a chromosome. (read mapped in proper pair)

For filtering a bam file what "samtools view" flags to be used? Some I come accross are

1. -F 2
2. -F 1806

aditionally we can also apply quality threshold too.

My question is whether to retain mate unmapped or singletons? as discordant reads.

All inputs on this topic is highly appreciated

Answer 1

[Junfeng]

I would like to know whether you have solved the problems. The discordant pairs are the pairs with incorrect orientations or the pairs with mapped distance beyond a fixed range (Ruibin Xi, Tae-Min Kim and Peter J. Park. Detecting structural variations in the human genome using next generation sequencing. Briefings in Functional Genomics; 2010; 9(5-6): 405-415).

[Rm]

thanks for the reference.

Answer 2

[Chris Whelan]

For "whether to retain mate unmapped or singletons as discordant reads", I think it is going to depend on what the SV caller you are using expects. I don't believe that either Hydra or SVDetect use pairs in which only one end is mapped as part of their algorithms (someone please correct me if I'm wrong on that!). Other tools, like Pindel, I believe, use those types of pairs. So I think you need to customize your workflow to the SV caller(s) you are planning to use.