Hi folks,
I'm looking at the 1000 genomes data using samtools. So far the flag filter has been great in helping me locate regions of interest, but for what I want to do next, I'm not sure this is the easiest/best option... Is there anyway to search for paired end reads that span a specific location, ie, one read would be to the left of the location in question, and the other read would be to the right of the location in question? Both reads would have to map properly. I suspect that at certain locations individuals are polymorphic for an insert, and the presence/absence of such reads as described above would confirm/deny this.
Apologies if this has already been addressed - I suspect I may not be searching using the correct terminology as I find it hard to believe I'm the only person interested in this!
All help gratefully received!
A
I'm looking at the 1000 genomes data using samtools. So far the flag filter has been great in helping me locate regions of interest, but for what I want to do next, I'm not sure this is the easiest/best option... Is there anyway to search for paired end reads that span a specific location, ie, one read would be to the left of the location in question, and the other read would be to the right of the location in question? Both reads would have to map properly. I suspect that at certain locations individuals are polymorphic for an insert, and the presence/absence of such reads as described above would confirm/deny this.
Apologies if this has already been addressed - I suspect I may not be searching using the correct terminology as I find it hard to believe I'm the only person interested in this!
All help gratefully received!
A
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