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012 genotype matrix using vcf tools

Hello everyone,

I have a vcf-file contains nearly 11millions SNPs. I want to convert my vcf file into 012 genotype matrix for LD pruning. I am using this code:

/data/programs/vcftools_0.1.13/bin/vcftools --vcf my.file.vcf
--012  --out output_geno.vcf

So, I get the output, but I am confused. According to manual the output 012 genotype matrix rows are individuals and columns are genotypes. I have 11million SNPs, should not get 11million columns (one columns per SNP)? when I count number of columns it is only nearly one million! Is there anything wrong or am I doing a ridiculous mistake?

Thanks for any help to figure out my mistake

vcftools genotype-matrix
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updated by Ram Ram • written by Ana Ana

Did you check the *.indiv and *.pos files that are also output with the --012 parameter? The *.indiv file should obviously cotain the expected number of samples that were in the input VCF.

Also, check the log file that's produced, particularly the line:

"After filtering, kept X out of a possible Y Sites"

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

How did you count the columns?

If you do something like this:

head -n 1 file.012  |  awk '{print NF}'

Do you have the right number of columns?

• 0 views • link
written by shinken123 shinken123

1 answer

The 012 output is n-by-features, rather than features-by-n. That means that each row is an individual and each column is a snp.

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written by Jautis Jautis

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