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

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

Hi Dr. Li,

Thank you for the feedback.
For my data, I used BWA for mapping and GATK for SNP calling.  What will be
the best practice for applying psmc to my data?  Should I just use BWA to
produce a SAM and convert it to a BAM, and then use samtools to convert the
BAM to fatsq for psmc?

Thanks,

Chih-Ming

On Fri, Dec 21, 2012 at 9:31 PM, Heng Li <lh...@sa...> wrote:

> 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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