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Is there any script or tool to Map gene SNP positions to genome coordinates

Is there any script or tool to Map gene SNP positions to genome coordinates, for example

CHROM     POS     ID    REF    ALT
1         60      .     A      T

60 is snp position in genes not chr 1

Now I want to find position of A in chr1, mean genomic position, of variant position in chromosomes not with in gene

for example gene start at 10000 position of chr1 , than inplace of 60 come 10060 mean genomic position of this variant. Please have any idea about it?

snp vcf sequence script
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updated by Ram Ram • written by misbahabas • misbahabas

genomax wrote that for everybody else who tries to make sense of your question because you fail EVERY TIME to provide important context to your post.

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written by WouterDeCoster WouterDeCoster

1 answer

If you can convert that to HGVS you can use it as input for the VEP, which will give you genomic coordinates in the output.

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written by Emily Emily

This is not a single species VCF. OP has done a multiple sequence alignment of sequences from an unknown number of species. I don't think we know if human sequences are involved.

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written by GenoMax GenoMax

My job here is to answer the question as stated, which is useful to anyone else who stumbles across this. If the OP is actually asking a different question to the one stated, that's on them.

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written by Emily Emily

Exactly, and the past threads I have tried to tell OP that he has to explain the context of his question. It's just impossible to have OP write what he wants and what he has done in one post. Anyway, this is the last thread I put some effort in understanding this.

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written by WouterDeCoster WouterDeCoster

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