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!
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!
Comment