Is there any script or tool to Map gene SNP positions to genome coordinates
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6.8 years ago
misbahabas ▴ 70

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 • 2.3k views
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Refer to this previous thread from misbahabas to get background information essential for this thread: Is it possible to annotate single genes by snpeff

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that thread is not usefull for me

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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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6.8 years ago
Emily 23k

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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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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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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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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