Question: Edge case in VCF format
0
gravatar for Will
4.7 years ago by
Will4.5k
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 http://samtools.github.io/hts-specs/VCFv4.2.pdf 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:

>Ref
ATTTGT
>Query
-TTTGT

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 • 1.1k views
ADD COMMENTlink written 4.7 years ago by Will4.5k

duplicate of Interpreting Gaps at Pos 0 in Terms of VCF

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum121k

Yup, had the wrong search terms.

ADD REPLYlink written 4.7 years ago by Will4.5k
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