How to get million target snps info(ie. chromosome, location) in a easy way?

Question

[Huichen03]

Hi all,

I am trying to get SNP locations. What I have done is that downloaded the dbsnp database in the ensembl and used the command line grep -f snps.txt homo_sapiens_snp.vcf > matches.vcf to get my target SNP info. There are about two million SNPs in my snps.txt, and all snps info in dbsnp database are stored in the file "homo_sapiens_snp.vcf". The problem is that the process got to be Killed and I cannot get the snps' locations. Do you guys know how to fix this?

Thank you in advance!

[h.mon]

Try the suggestions from the thread Question: how to get a subset of vcf file for specific SNPs.

Please tell us if those work or not. If they don't, also tell us how much memory do you have available.

Answer 1

[Alex Reynolds]

One way to do this is via the command line. You could download SNP annotations via wget. For example:

$ wget -qO- ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/common_all_20180423.vcf.gz | gunzip -c | convert2bed --input=vcf --output=bed --sort-tmpdir=${PWD} - > hg19.snp151.bed

Filter via grep for the SNP of interest. For example, to search on a single SNP ID:

$ grep -F rs554008981 hg19.snp151.bed
1       13549   13550   rs554008981     .       G       A       .       RS=554008981;RSPOS=13550;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000026000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9966,0.003395,.;COMMON=1;TOPMED=0.99221139143730886,0.00778064475025484,0.00000796381243628

To search on a file of IDs, e.g. a list of SNP IDs in rsIDs.txt:

$ grep -fF rsIDs.txt hg19.snp151.bed > matches.bed

[Huichen03]

Hi, Thank you for your advice. When searching on a file of IDs, should the command line be $ grep -f? If I use $ grep -fF, I will have the error that grep: F: No such file or directory.

[Alex Reynolds]

You need a file of IDs, stored in the file rsIDs.txt (for example).

Answer 2

[finswimmer]

Hello,

I asked a similar question some time ago. You could try one of the answers there. Especially the way I found on github of htslib and reported in the thread looks promising to me.

fin swimmer