This is a test version of Biostars. For the public version, visit https://www.biostars.org.
find reads information in .vcf file

Hi all,

I was wondering if is possible to have reads identification(Id/name) in .vcf file? It might be useful, for instance, when you pick two following variants and want to check how the specific read match the variants?
I didn't find any related information in .vcf specification, but still hope there is some option, or even some tool to do so?

Thanks for any information

vcf
• 3,295 views • link
updated by Ram Ram • written by lebedana21 • lebedana21

1 answer

instead of generating a huggge vcf containing the name of the reads a better idea is to look back in the bam to find the variants: e.g : How to extract reads with a known variant form a bam file Extract reads with variant at given position Finding The Number Of Reads Which Support A Variant In Vcf ...

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you Pierre for response,

I had checked all of the tools. However, no seems suitable for my goal. In particular, I need to call all variants (not just a couple, mb my example was confusing, sorry for that), and preserve information about reads for each allele for each variant.
For instance, if alleles (SNP) at the third position (pos3) are A and T, e.i. --A-- and --T--, and the read R1 is GGAGG, then I got as an output pos3: R1=A (easy for a SNP, more complicated in other cases). The output format is so, since I will need to iterate through variants, not through reads.

• 0 views • link
written by lebedana21 • lebedana21

Log in to answer this question.

More posts like this