Obtain chromosome, position, and alleles based on a list of SNP names

Question

[jiumeng66]

I have a SNP list (including 3660 SNPs), which have only the name, like rs41457244.

Now I need the other information of the SNPs, such as chromosomes, positions (hg19), and alleles. What can I do?

The following is part of my SNP list:

 rs2088175
 rs2983855
 rs2821958
 rs41469446
 rs619987
 rs2877425
 rs41447048
 rs41497748
 rs503808
 rs386628
 rs6667995
 rs41405345

[Bioinformatics_NewComer]

Try rsnps package in R

https://cran.r-project.org/web/packages/rsnps/rsnps.pdf

[Ram]

Please add an example/more detail or move your suggestion to a comment. Thank you!

[Bioinformatics_NewComer]

Added link for the package tutorial.

[Ram]

IMO it still needs work to qualify as an answer. The package name and package manual link are effectively just a suggestion now. I'm moving this to a comment.

Answer 1

[Pierre Lindenbaum]

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select chrom,chromStart,chromEnd,name,alleles,alleleFreqs from snp150 where name in ("rs2088175","rs2983855","rs2821958","rs41469446","rs619987","rs2877425","rs41447048","rs41497748","rs503808","rs386628","rs6667995","rs41405345")'
+---------------------+------------+-----------+------------+---------+--------------------+
| chrom               | chromStart | chromEnd  | name       | alleles | alleleFreqs        |
+---------------------+------------+-----------+------------+---------+--------------------+
| chr3                |   76216220 |  76216221 | rs2088175  | C,G,    | 0.875399,0.124601, |
| chr21               |   13597605 |  13597606 | rs2821958  | A,G,    | 0.884181,0.115819, |
| chr4                |   68990362 |  68990363 | rs2877425  | A,G,    | 0.085463,0.914537, |
| chr4_GL000257v2_alt |     566381 |    566382 | rs2877425  | A,G,    | 0.085463,0.914537, |
| chr10               |   38291051 |  38291052 | rs2983855  | C,T,    | 0.468850,0.531150, |
| chr6                |   28816618 |  28816619 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000250v2_alt |      82197 |     82198 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000251v2_alt |     307169 |    307170 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000252v2_alt |      82220 |     82221 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000253v2_alt |      82185 |     82186 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000254v2_alt |      82211 |     82212 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000255v2_alt |      82201 |     82202 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr6_GL000256v2_alt |     125864 |    125865 | rs386628   | C,T,    | 0.339257,0.660743, |
| chr17               |   22206798 |  22206799 | rs41447048 | C,T,    | 0.833067,0.166933, |
| chr18               |   14208563 |  14208564 | rs41469446 | A,G,    | 0.868011,0.131989, |
| chr1                |   83314732 |  83314733 | rs41497748 | A,T,    | 0.831669,0.168331, |
| chr2                |  126689276 | 126689277 | rs503808   | A,G,    | 0.647364,0.352636, |
| chr1                |  149015643 | 149015644 | rs619987   | A,T,    | 0.869010,0.130990, |
| chr1                |  205854053 | 205854054 | rs6667995  | A,C,    | 0.758586,0.241414, |
+---------------------+------------+-----------+------------+---------+--------------------+

[jiumeng66]

thank you so much. but in my terminal, the command return "-bash: mysql: command not found". Dose it mean that some tool need be installed?

[Pierre Lindenbaum]

Dose it mean that some tool need be installed?

ubuntu:

apt-get install mysql-client

[zx8754]

They have 3660 SNPs. Any way to automate this bit of sql code: ... in ("rs2088175","rs2983855","rs2821958", ... "rs_TheLastSNP")' ?

[Ram]

They can use sed. With an ID-per-line file, replace each line with "\1", then use tr to replace newlines with commas. An additional sed to delete the last comma might be required.

Note: Exact code not provided to encourage learning

Answer 2

[Emily]

BioMart

Use the short variation database, filter by your list of IDs, get location and alleles as attributes.

Example query

Answer 3

[igor]

There are a lot of excellent responses already, but I wanted to offer an alternate solution.

You can also download SNPs in a table format from UCSC: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp150.txt.gz

Since these are in a table format, they are a little easier to read and process without specialized tools. For example, you can run:

zcat snp150.txt.gz | grep -w -f snplist.txt

Where snplist.txt is your list of SNPs.

Answer 4

[Bastien Hervé]

If you download the dbSNP of your genome, you will have all the informations you need. Just look into the dbSNP file with your SNPs list using Awk, Python, Perl...

[jiumeng66]

Thank you, but where can I download the dbSNP?

[Bastien Hervé]

hg19 :

In your browser

ftp://[e-mail]/bundle/hg19/dbsnp_138.hg19.vcf.gz

or in your terminal

wget ftp://[e-mail]/bundle/hg19/dbsnp_138.hg19.vcf.gz

[jiumeng66]

sorry to reply lately, I have download it just now with your help. Thank you very much.

Answer 5

[Alex Reynolds]

If you want to do things locally, you can make a searchable resource you can query as you like.

1) Get SNPs and write them into a text file sorted by SNP ID.

For hg19, for instance, using BEDOPS convert2bed to convert VCF to BED:

$ LC_ALL=C
$ wget -qO- ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/All_20170710.vcf.gz \
   | gunzip -c \
   | convert2bed --input=vcf --sort-tmpdir=${PWD} - \
   | awk -v OFS="\t" '{ print $4,"chr"$1,$2,$3,$6,$7; }' \
   | sort -k1,1 \
   > hg19.snp150.sortedByName.txt

This text file includes the SNP rsID, the genomic position, and the reference and alternate alleles. It is sorted by the SNP rsID, a property which we will use to enable fast searches.

2) Install pts-line-bisect, which does a binary search on lexicographically-sorted files, such as the one that was just made:

$ git clone https://github.com/pts/pts-line-bisect.git
$ cd pts-line-bisect && make && cd ..

Binary searches are pretty fast and great for write-once, read-many applications like this.

3) Run a query. The following command would return a six-column BED file:

$ rs_of_interest=rs41457244
$ ./pts-line-bisect/pts_lbsearch -p hg19.snp150.sortedByName.txt ${rs_of_interest} \
   | head -1 \
   | awk -v OFS="\t" '{ print "chr"$2,$3,$4,$1,$5,$6; }'

Step 3 can be put into a script so that you can re-run it with your SNP of interest on demand.

For instance:

#!/bin/bash
pts_lbsearch_bin=./pts-line-bisect/pts_lbsearch
sorted_snp_txt=hg19.snp150.sortedByName.txt
${pts_lbsearch_bin} -p ${sorted_snp_txt} $1 | head -1 | awk -v OFS="\t" '{ print "chr"$2,$3,$4,$1,$5,$6; }'

Then:

$ ./search_snps.sh rs41457244
...

If you have a file of rs* IDs, you could loop through them via bash:

$ while read rsID; do ./search_snps.sh $rsID; done < snpIDs.txt | sort-bed - > snps.bed

Writing a sorted BED file can be useful for enabling set operations with BEDOPS and other toolkits.

[jiumeng66]

Thank you, it is a little bit complex. I will try.^_^

[Alex Reynolds]

No need, if the other solutions work for you. Once set up, however, it is just a way to query stuff very quickly, repeatedly, without going over a potentially slow network. Lots of great options here, regardless.