Question: Edge case in VCF format
gravatar for Will
4.3 years ago by
United States
Will4.5k wrote:

I'm trying to create a VCF formatted file from a pairwise alignment of two genomes. Downstream I'm going to use this to calibrate some deep-sequencing data where I know the input sequence (and thus the variants).

I'm just running into an odd edge-case in the VCF format. Following the specifications described in I'm running into the edge-case where there is a "gap" in the first base of the query sequence with respect to the reference:


Based on my understanding of the the VCF format I need to put the preceding & current base in the "REF" column and the preceding base in the ALT column. The POS should also be 0?

Any suggestions?

alignment • 996 views
ADD COMMENTlink written 4.3 years ago by Will4.5k

duplicate of Interpreting Gaps at Pos 0 in Terms of VCF

ADD REPLYlink written 4.3 years ago by Pierre Lindenbaum116k

Yup, had the wrong search terms.

ADD REPLYlink written 4.3 years ago by Will4.5k
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: 1129 users visited in the last hour