vcf to fastq conversion loosing information on heterozygotes

[Rcucullatus]

Hi there,

I want to generate a fastq file with information on heterozygotes from a single individual genome to input into Heng Li psmc software. I can create a vcf file from reads mapped to a reference sequence fine, with all the heterozygote positions discriminated, but when I convert this to fastq, I get only one consensus sequence, without heterozygotes. I have tried conversion commands in samtools:

vcfutils.pl vcf2fq mappedreads.vcf > mappedreads.fq

and the

vcfutils.pl vcf2fq -D 100 mappedreads.vcf > mappedreads.fq

both of which produce fastq file just fine, but again, no apparent information on heterozygous position.

I also checked samtools manual, but there doesn't seem to be much information on the vcf2fq application, so I'm a bit stuck.

Anyone can help me with this?

Thanks!

[mayukhmondal]

Heterozygote information are there as:
AC=>'M', AG=>'R', AT=>'W', CA=>'M', CG=>'S', CT=>'Y',GA=>'R', GC=>'S', GT=>'K', TA=>'W', TC=>'Y', TG=>'K'