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

[Heng Li <lh...@sa...>]

Firstly, there is no way to convert a SNP-only VCF to consensus sequence as you do not know which bases are callable. Secondly, even if you have an all-site VCF, you cannot use GATK as it does not compute consensus quality which is necessary for generating consensus sequence.

Heng

On Dec 21, 2012, at 1:07 AM, Hung Chih-Ming wrote:

> 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 
> 
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