converting vcf to text file

Question

[AB]

Hi,

I want to run Matrix EQTL on my data. I have the genotype information as an imputed VCF file and matrix EQTL requires a Snp.txt file. How can convert the vcf to a text file ??

Thanks, Apoorva

[Pierre Lindenbaum]

A vcf IS a text file. You have to show us what is the format of this 'snp.txt' file.

[AB]

So this is the format of the snp.txt file as required by Matrix EQTL R package. The description only says the file should have the genotype information for the markers across all the samples

id  Sam_01  Sam_02  Sam_03  Sam_04  Sam_05  Sam_06  Sam_07  Sam_08  Sam_09  Sam_10  Sam_11  Sam_12  Sam_13  Sam_14  Sam_15  Sam_16
Snp_01  2   0   2   0   2   1   2   1   1   1   2   2   1   2   2   1
Snp_02  0   1   1   2   2   1   0   0   0   1   1   1   1   0   1   1
Snp_03  1   0   1   0   1   1   1   1   0   1   1   0   1   1   1   2
Snp_04  0   1   2   2   2   1   1   0   0   0   1   2   1   1   1   0
Snp_05  1   1   2   1   1   2   1   1   0   1   1   2   0   1   2   1
Snp_06  2   2   2   1   1   0   1   0   2   1   1   1   2   0   2   1
Snp_07  1   1   2   2   0   1   1   1   1   0   2   2   0   1   1   1
Snp_08  1   0   1   0   1   0   0   1   1   1   0   2   0   1   1   1
Snp_09  2   1   2   2   0   1   1   0   2   1   1   0   1   1   0   0
Snp_10  1   1   0   0   0   2   2   1   1   2   1   1   1   1   1   0
Snp_11  2   2   2   0   2   1   1   2   1   2   0   1   0   1   1   2
Snp_12  1   1   2   2   2   1   1   1   1   0   2   0   1   1   0   2
Snp_13  0   1   1   1   1   1   2   1   2   2   0   0   0   1   1   1
Snp_14  0   0   1   0   1   2   2   2   1   1   1   0   1   0   1   0
Snp_15  1   2   1   2   2   1   2   1   1   2   1   1   1   2   0   2

The vcf file I have is in this format.

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  P01497  P01509
1   10177   1:10177 A   AC  .   PASS    AF=0.42372;MAF=0.42372;R2=0.00241;AN=2;AC=0 GT:DS:GP    0|0:0.827:0.344,0.485,0.171 ./.:.:.
1   10235   1:10235 T   TA  .   PASS    AF=0.00119;MAF=0.00119;R2=5e-05;AN=2;AC=0   GT:DS:GP    0|0:0.002:0.998,0.002,0 ./.:.:.
1   10352   1:10352 T   TA  .   PASS    AF=0.43825;MAF=0.43825;R2=0.00238;AN=2;AC=0 GT:DS:GP    0|0:0.863:0.323,0.491,0.186 ./.:.:.
1   10539   1:10539 C   A   .   PASS    AF=0.0007;MAF=0.0007;R2=0.00315;AN=2;AC=0   GT:DS:GP    0|0:0.001:0.999,0.001,0 ./.:.:.

[cpad0112]

There are certain problems with your VCF and requested output.

For eg. for first record:

1   10177   1:10177 A   AC  .   PASS    AF=0.42372;MAF=0.42372;R2=0.00241;AN=2;AC=0 GT:DS:GP    0|0:0.827:0.344,0.485,0.171 ./.:.:.

1. Reference allele is A and alternate allele AC. Both are different alleles. However for sample P01497, your GT 0|0. 0|0 means you have reference alleles on both chromosomes (maternal and paternal). I am not sure if this information is correct. Unless it is A to A,C (A in some and C in some. For this sample P01497, it is A)
2. In desired matrix, you have only one Genotype information for a given SNP and given sample. But in your VCF, you have two genotypes. At this point, I assume that you need sample Alt allele in Sample. Please confirm.

[Pierre Lindenbaum]

In desired matrix, you have only one Genotype information for a given SNP

@cpad0112 I think it uses a integer notation for the genotypes: 0=HOM_REF, 1=HET, 2=HOM_VAR

[cpad0112]

Thanks @Pierre. Does that mean GT information in VCF needs to be reformatted to 0=HOM_REF, 1=HET, 2=HOM_VAR format (for each SNP /Sample) via a third party tool or code?

[cpad0112]

can you post your VCF headers as well here?

[cpad0112]

to convert vcf to tsv, use vcf2tsv from vcflib

Answer 1

[AB]

This post here has a very similar question

How to interpret and extract from a Vcf file Genotype informations as values

However, i just read in my VCF file into R using the vcfR package, converted it into a dataframe and manually changed the genotype information.

Also, as mentioned in one of the comments in that post, vcf-to-tab can be used to convert the vcf to a table and writing a script to convert.