Question: Calling TE sequences from VCF files
gravatar for elcortegano
10 months ago by
elcortegano50 wrote:

I have run the software sniffles to call structural variants from Pacbio sequences. In the resultant VCF file, most of entries in the ALT field look like:


In the example above, this is actually for a variant in a different chromosome, CHR=chromosome_1 and POS=270281, so I guess this is a transponible element coming from chromosome 3 that is present in that location.

I am not familiarized with this format for the ALT field, and was wondering if there is a straightforward way to get the sequence for that element (or any other structural variant found in the VCF). Any ideas?

ADD COMMENTlink modified 10 months ago • written 10 months ago by elcortegano50
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 959 users visited in the last hour