1000 genome project specific genes selection
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9 weeks ago
Eliza ▴ 30

Hi,

I was wondering is there any way to get the data for specific genes from the 1000genome project instead of downloading all the mutations in a specific chromosome, (If I have a lists of genes I'm interested in can I download only the SNPs in those genes without downloading the data for the entire chromosome)?

For example if I'm interested in AUTISM there are SNPs found on GWAS but they are spread over multiple chromosomes. Is there a way to download all the SNPs in the genes associated with AUTISM?

Thank you

gwas 1000genomes • 238 views
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1
Entering edit mode
9 weeks ago
bk11 ★ 2.3k

You can try Data Slicer unless you have too many reasons to pull from.

OR

Alternatively, you can use tabix to get list of SNPs of a region from 1000 genome as follows:

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-49967768 |cut -f1-5 |awk '!/##/' |head
#CHROM  POS ID  REF ALT
2   39967768    rs11124691  T   A
2   39967778    .   G   C
2   39967793    .   C   T
2   39967824    rs114023135 C   T
2   39968061    .   G   A
2   39968140    rs72936091  C   T
2   39968210    rs6716262   G   T
2   39968231    rs78390685  T   A
2   39968486    rs118064218 T   A
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