how to find snps within 1Kb from the gene

Question

[mms140130]

Hello,

I have asked similar question but the answer was complicated, is there an easy way to download such data, I used to use Scandb , which I download the data from the website but I found that they use different snps annotation than what I have , mine is hg19. so the position is different

Is there a website where I can download such data in .txt file

Thank you,

[finswimmer]

Hello,

it is not clear to me what you are looking for. Something like the Variant Table provided by ensembl for every gene?

Please describe more detailed what you have and what you want to get.

fin swimmer

Answer 1

[Alex Reynolds]

Via BEDOPS tools and UCSC data, you can:

1) Get SNPs for your reference genome:

$ wget -qO- http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp142Common.txt.gz \
    | gunzip -c - \
    | cut -f2,3,4,5,10 - \
    | awk -v OFS="\t" '{ print $1, $2, ($2 + 1), $4, $5 }' - \
    | sort-bed - \
    > hg19.snp142.bed

2) Get gene annotations; for example, from Gencode:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz \
    | gunzip -c - \
    | gff2bed - \
    | awk '($8="gene" && $4!~/^exon/)' - \
    | cut -f1-6 - \
    > hg19.gencode19.genes.bed

3) Do a bedmap operation to map hg19 SNPs within 1kb of hg19 gene annotations:

$ bedmap --echo --echo-map-id-uniq --delim '\t' --range 1000 hg19.gencode19.genes.bed hg19.snp142.bed > answer.bed

The file answer.bed contains genes and all rs* IDs of SNPs that fall within 1000 upstream or downstream of each gene interval.

[mms140130]

is the gene annotation is for hg19 ?

[Alex Reynolds]

Yes, it is for hg19. You can visit the Gencode site to confirm.

[mms140130]

where can I download sort-bed ?

[Alex Reynolds]

It is part of the BEDOPS toolkit I linked to. You can go to that link and read instructions on where to get it and how to install it.

[mms140130]

I got the following error from the below command

wget -qO- http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp142Common.txt.gz \
    | gunzip -c - \
    | cut -f2,3,4,5,10 - \
    | sort-bed - \
    > hg19.snp142.bed

Error on line 1 in -. Genomic end coordinate is less than (or equal to) start coordinate

[Alex Reynolds]

See modified answer. I added one to each SNP position to that it conforms to how BED coordinates are represented.

[mms140130]

Thank you Alex, can I ask a question is this solution will give the same output as in C: Download snps within 1Mb from gene

but changing the 1 mb to 1 kb ?

your solution here gave me small number of snps per gene, in the C: Download snps within 1Mb from gene

I had more snps per gene and i applied 1kb for both solutions, what is the difference?

which code to trust

[Alex Reynolds]

It looks like you asked that question, too. The options specified are different, the reference genomes are different and so the inputs are different, and the two answers use different ranges. I would say you should review the links to documentation to understand the options, and review the inputs to verify them, and then decide what answer you trust, if any, based on what options you're using and what inputs you're providing.

[mms140130]

Thanks for your comment it helped

Can ask you what is the difference between snp 147.txt and 142common .txt

which one should I choose ?