Getting the read names/ IDs?

Question

Getting the read names/ IDs?

Opened this issue 4 years ago · 4 comments

Hello,

I was wondering if there was a way to get the read names for each base. For example, let's say at the position 237 there are 20 reads supporting A and 10 supporting C, is it possible to have the names of the reads supporting the A and the names of the reads supporting the C?

Answer 1 · 2020-07-20T13:02:37.000Z

I would like this feature too...
@aderzelle Did you find another way to do this ?

Answer 2 · 2020-07-20T13:06:05.000Z

@dridk
I found bamql
https://github.com/BoutrosLaboratory/bamql
it does have an option, nt_exact, to specify what nucleotide value you want at position x, relative to the chromosome coordinates.
It is slow, though

It could be that https://github.com/vibansal/HapCUT2
also gives that, one would need to parse the compact frag file I guess (I haven't looked into it yet).

Answer 3 · 2020-07-20T14:01:27.000Z

Whaoo ! Bamql is awesome !
I added your suggestion on biostar ! https://www.biostars.org/p/322664/#450406

Answer 4 · 2020-07-20T14:05:43.000Z

yes, I don't really understand why it does not have more use ^^'

could be very few people need to make such specific queries, I guess.