Affymetrix Genotyper Console Output Using For Plink Run Of Homozygosity

Question

[Msa]

Dear all, I have a .txt file (includes Chrom, Position, SnpId, Genotype) from Affymetrix Genotyper Console (Affymetrix SNP Array 6.0). Normally we put this into the webtool "Homozygosity Mapper" and we get a Genome-wide homozygosity plot. Now I should try to do the same with PLINK - run of homozygosity. I rearranged the .txt file so that it matches the .ped file for PLINK (but only for one individual, if I have more, should I merge the .ped files?). Neither the .ped files nor the .map files contain the Genotypes, so how is it possible for PLINK to make this "runs of homozygosity"?

Thank you very much for your help, best regards, msa

[Matt Shirley]

The PED files actually do contain genotypes. Each row begins with annotation information in the first six columns (see my answer below), and then continues with the genotype of that individual over all markers. The MAP files contain the annotation for markers. Once you have your genotypes in a PED file (a single PED file can contain genotypes from multiple individuals, one per line) and your MAP file, you can run PLINK. You should take care that you are not looking at the definition of a TPED, as that does not contain genotypes.

Answer 1

[Matt Shirley]

Some of this content is from the PLINK data formats page.

<---- normal.ped ---->
1 1 0 0 1  1  A A  G T
2 1 0 0 1  1  A C  T G
3 1 0 0 1  1  C C  G G
4 1 0 0 1  2  A C  T T
5 1 0 0 1  2  C C  G T
6 1 0 0 1  2  C C  T T

The above is a typical PED file. It includes the following columns: [?] Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female; other=unknown), Phenotype.

<--- normal.map --->
1  snp1   0  5000650
1  snp2   0  5000830

The MAP file (above) specifies the layout of the chip and has the columns: [?] chromosome (1-22, X, Y or 0 if unplaced), rs# or snp identifier, Genetic distance (morgans), Base-pair position (bp units).

Note that for your data, a TPED and TFAM may be more appropriate. T stands for transposed, and that just means that your genotype data will populate columns instead of rows. If you construct either a PED or TPED you can use plink --file data --recode --transpose to convert to the reciprocal format.

You will then want to look at the runs of homozygosity workflow. Hope this helps.