How to get a list of genes from a list of SNPs
I have a snp_list.txt file, which contains 49.663 lines, one for each SNP typed by a canine SNP-chip. The file includes 6 columns for each line, and looks like this:
ProbeId Chr Pos BroadID Allele1 Allele2
chr1.3398480 1 3398480 BICF2P391650 C T
chr1.3453895 1 3453895 BICF2G630707948 C T
chr1.3573121 1 3573121 BICF2P1282632 G T
chr1.3691446 1 3691446 BICF2G630708020 C T
chr1.3699781 1 3699781 BICF2G630708023 A C
chr1.3713883 1 3713883 BICF2G630708027 G T
Now, what I'd like to know is if there is a way to get the list of canine genes in which these SNPs are included, based on the informations present in the snp_list.txt file.
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Nuthatch •
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Convert the list into a BED file and then intersect it with a BED or GTF containing the genes. You can use
bedtools intersectfor this. Please try out something, and then come back if you get stuck.