[Samtools-help] Fwd: from vcf to consensus sequence file

[Hung Chih-M. <ym...@gm...>]

Hi

>From the website I understand the commend line below converts the input BAM
to a BCF format*, *then converts BCF to VCF, and finally to fastq.
$ samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - |
vcfutils.pl vcf2fq > cns.fq


I am wondering whether there is a way I can just input a VCF file (produced
by GATK) instead of a BAM file and convert it to a fastq file?
What I really want to do is based on SNP data to infer population history
using psmc (by Heng Li).  Psmc requires fastq input, not cvf, files.  So, I
am looking for a way to convert the vcf file (SNP calling data from GATK)
to fastq.

I appreciate any comments,

Thanks,

Chih-Ming