Tped file locus column to gene
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3.7 years ago
storm1907 ▴ 30

Hello, I need to convert second column in tped file - from location to gene name. Such as: from

1   chr1:183189 0   183189  G   C
1   chr1:609407 0   609407  0   0
1   chr1:609434 0   609434  0   0
1   chr1:609435 0   609435  G   G

to

1   TPP1    0   183189  G   C
1   TPP1    0   609407  0   0
1   TPP1    0   609434  0   0
1   TPP1    0   609435  G   G

Files are made in GRCH38 build. I think, I need to find a tool, that compares second column of chromosomal position with a genome reference sequence and outputs same file with gene names (preferrably in HGNC nomenclature, not Ensemble format). I am confused, which tool is best for this purpose: Bedtools or BCFtools, or any other? I tried to look in this forum for similar issue, but could not find appropriate solution

Thank you!

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