gtc to plink ped format - 0|G instead of A|G

[1teaspoon]

Hi folks,

I am having an issue when using IlluminaBeadArray libaray to convert gtc file to ped file format. A lot of snps in the converted plink file have 0|G instead they should be A|G. Below is the part of my script related to this conversion.

import sys
import os
from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype

def outputPlink(gtc_file, manifest_file, sample_name, plink_out_dir, genoThresh = 0.15):
manifest = BeadPoolManifest(manifest_file)
gtc = GenotypeCalls(gtc_file)
GenoScores = gtc.get_genotype_scores()
top_strand_genotypes = gtc.get_base_calls()
outBase = plink_out_dir + '/' + sample_name
allGenotypes = []
with open(outBase + '.ped', 'w') as pedOut, open(outBase +'.map','w') as mapOut:
for (name, chrom, map_info, source_strand_genotype, genoScore) in zip(manifest.names, manifest.chroms, manifest.map_infos, top_strand_genotypes, GenoScores):
mapOut.write(' '.join([chrom, name, '0', str(map_info)]) + '\n')
if source_strand_genotype == '--':
geno = ['0', '0']
else:
geno = [source_strand_genotype[0], source_strand_genotype[1]]
allGenotypes += geno
pedOut.write(' '.join([sample_name, sample_name, '0', '0', '0', '-9'] + allGenotypes) + '\n')

[jjzieve]

@1teaspoon Can you post the entire script? Or better, open a branch? And which product are you running? Just looking at the code, I can't really tell what might be going wrong. I'd assume top_strand_genotypes would be populated with with actual string base calls based on get_base_calls (

BeadArrayFiles/module/GenotypeCalls.py

Line 378 in dc4eb37

def get_base_calls(self):

) so not sure where a "0" came up. But hard to say without reproducing what you're running and stepping through the code.