What are the rules Pindel uses to determine which pairs of reads it will use?

Question

[mohesan]

I am trying to determine how Pindel decides on which (pair)reads it uses to analyse for structural variances. Pindel takes in a bam file that has been aligned using BWA. Pindel then applies the pattern-growth method,to find indels, on reads that could not be mapped but their pair was mapped successfully as well as on reads that BWA matched both pairs successfully but found an indel on them. According to the BWA aligned bam files that I am working with, there are reads that support an indel but Pindel does not return these reads when I run it. My question is: What are the rules Pindel uses to determine which pairs of reads it will use? Any help at all will be appreciated! Thanks!

[mohesan]

For example should there be a certain MS score(i doubt this is the case)?

Answer 1

[liangkaiye]

When you say Pindel does not use these reads, what kind of the reads you are referring to? Is it discordant read pair or the other type of difficult-to-map reads?

[mohesan]

I am not sure. Is that a possible reason for them to remove reads?

[mohesan]

Majority of the reads that Pindel did not use were mapped in proper pair