Closed edawson closed 3 years ago
Hi Eric,
Your intuition was correct. We also normalize the variants according to NGS conventions (left align). The entire process for creating the variant ID looks like this:
Step | Result |
---|---|
1. original VCF alleles | chr1 66572 . GTA GTACTATATATTATA |
2. trimmed alleles | chr1 66575 . - CTATATATTATA |
3. left aligned alleles | chr1 66573 . - TACTATATATTA |
4. add back the padding base | chr1 66572 . G GTACTATATATTA |
Here's a visual depiction of the alignment process. Notice that we're really just changing the location of the genomic TA
alleles.
Ah, I see. This was very helpful and a really interesting one once you showed the ref bases - thanks!!
Hi,
When reviewing the docs, I noticed I had some confusion around an example in the canonical variant id portion.
The final variant listed in the docs appears to have an incorrect reference allele in the variant ID of the second allele:
Did I perhaps not left-align + trim this correctly in my brain? It looks to me like this variant id should read
1-66572-GTA-GTACTATATATTA
. If it were trimmed, I think it might read1-66575-A-ACTATATATTA
. Any clarification y'all might have on this would be great - thanks!