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Converting genotype file into bed format

Hi,

I have a problem. I have genotyping data for hundreds of thousands of snps and thousands of individuals. The coordinates are in hg17 and I need to convert them into hg19. Liftover is fine for this, but it works with bed files. So I need to convert my files into bed format, carry to hg19, then convert bed to genotyping format again.

If it was for a list of SNPs of several thousands, I can write a perl script for that. But for a dataset of this size, it will take too long because each line consists thousands of fields, so parsing would be slow. Is there a practical tool for this?

The file format is as follows:

identifier hg17_coordinate allele1 allele2 subject1_a1a1 subject2_a1a2 subject1_a2a2 subject2_a1a1 ...
rs1111 2564468 A G 1 0 0 0 1 0 ...

Thanks

genome snp
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updated by Ram Ram • written by yasin.delco • yasin.delco

1 answer

if you have chromosomes in your data set then replace "CHROM" with proper column number in 

awk '{print "CHROM", $2-1, $2, $1, $3, $4}' input > output

This should be quick. Then use liftover for bed, convert back to original format and replace first 4 columns (but where is the chromosome id in your data???

if there is no info about chromosomes, you might be able to get bed files by searching dbSNP for proper rsid in here ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/BED/ also I am nit sure if very old rsid will be in there.

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written by Petr Ponomarenko Petr Ponomarenko

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