genome browser to check SNP genome build
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7 weeks ago
rheab1230 ▴ 20

Hello everyone, I have a file containing SNP. I want to take this SNP and go to genome browser to see which gene is close to this SNP. Basically I want to know the genome build of my vcf files. Does anyone knows how to do that to check genome build of file using genome browser? Thank You.

build snp vcf genome • 297 views
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7 weeks ago
cmdcolin ★ 1.7k

Sometimes the creator of a VCF file may not tell you what genome build it is which is quite annoying in bioinformatics in general!

You could look at your VCF file in a text editor and look at the header lines and see if there is any mention of hg19 or hg38 or GRCh38 or GRCh37 or things of that sort (if you are referring to human data)

If it is not clear from the header, it may require some next steps e.g. looking at dbSNP IDs in the file, and then looking up that dbSNP ID e.g. rs123145 on NCBI, and seeing what the coordinate NCBI gives for hg38, and whether that matches what coordinate is in the VCF

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Yes, I checked the header and its not mentioned. Okay I will check out NCBI for the coordinates. Also do you have any idea if I can check the gene or rsid from genome browser?

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Random workflow idea. If you open the hg38 in the genome browser and open your track, and you zoom to a random place, click a variant, it has a rsID like rs1231513, then you google that and it tells you it is at a different position on hg38 but it matches on hg19, then you can change your genome browser to hg19

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