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
- -F 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