Hello, I have a VCF file of 816 individuals. I found a mutation carried by 1 individual. I have the chromosome position where I found a mutation and I would like to know the FASTA sequence/variation. I need to check whether it is truly this mutation that is the one located -141 (of the TSS of the gene) or not . Any help is appreciated.
If I understand you correctly, you have found a variant and are interested to know if it is the same as another variant that you found in the literature. The literature-derived variant is with respect to transcript coordinates and your variant is in chromosome coordinates. Unless you can translate one to the other, you may not be able to know with certainty if they are the same. You could grab all the TSS from a database (or multiple databases) in the vicinity of your variant and do some quick math to see if your variant is 141 bp upstream of any TSS.
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version 2.3.6
I think your question needs a little more specificity. It is not entirely clear what you are after. Getting a genomic content of an interval in a fasta file is a fairly straightforward task, though it is one with many alternative solutions.
But if you have a VCF file you already know what the reference is for that location so why would you need to obtain that base again? Your subsequent comment does not help either, it seems that you are after something else.
You are looking for the base at that location in the fasta sequence, or you are looking for previously-seen variants at that location? If the latter, what organism are you working with?
I am dealing with human variants. I actually found the variant (base) and I know the location however searching in the literature I found a previously reported variant in that gene noted as -141C>G. My question is how can I know whether these two are the same or not?