Convert From .Ped/.Map To Dosage Format

Question

[ellens2]

Hello,

I am trying to convert from .ped and .map files (output from PLINK) to some sort of gene-dosage format for use in an eQTL study (0 = homozygous minor, 1 = heterozygote, 2 = homozygous major.)

I tried coding this up myself, but ran into a problem when I discovered that I have no way of knowing which allele is major and which is minor. I have legend files listing "allele1" and "allele2", but by looking at dbSNP I discovered that there is no correlation between allele1/2 and major/minor.

I did see this answer : Conversion of ped/map or bim/bim/ fam files to dosage for GWAs mit Probable and comparison with imputated genotypes but I was not able to use genABEL because I don't know what an "infofile" is. (yes, I saw the answer someone posted to my question, but it didn't tell me what an "infofile" is.)

I tried using fcgene (http://sourceforge.net/projects/fcgene/) which claims to convert to dosage format, but this only gave me a list of SNPs as output!

Someone has to have written a ped->dosage conversion tool already, but I can't seem to find it. Could someone point me in the right direction?

Thanks!

Answer 1

[Joey]

You may want to use the --recodeA option in PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml). The output file will contains SNPs with 0,1 or 2 counts of the minor allele.

Answer 2

[zx8754]

This is infofile format:

1. SNP identifier from -g file (snp_id)
2. rsID (rs_id)
3. base pair position (position)
4. expected frequency of allele coded '1' in the -o file (exp_freq_a1)
5. measure of the observed statistical information associated with the allele frequency estimate (info) [details]
6. average certainty of best-guess genotypes (certainty)
7. internal "type" assigned to SNP (type)

As I understand you want to convert AA AB BB to dosage 0-2. As mentioned in this Conversion Of Ped/Map Or Bim/Bim/ Fam Files To Dosage For Gwas Mit Probable And Comparison With Imputated Genotypes I was able to do this in 2 steps, ped to gen then gen to mach. Infofile is not actually used when converting gen to mach. It is just an extra info when creating machinfo, whatever is given as infofile becomes machinfo file. So you infofile can be as basic as snp name, position.

Answer 3

[krish.hari.sharma]

Hi there! what command have you used exactly? please use the following command :

./fcgene --ped example.ped --map example.map --oformat R “--force ref-allele=minor-allele --out example