Entering edit mode
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!