Extracting a raw sequence from VCF files

[Sebastian]

Hi,

 

I wanted to ask if there is a simple way to extract the base sequence (A,C,G,T,N) for each chromosome and each individual from the korean dataset?

I would assume that given the reference sequence there should be an automated way getting raw sequences from a VCF file.

 

We are trying to implement an algorithm for SNP finding (Dataset 2, Question 1), but have only considered raw base sequence files as input so far.

 

Thanks

Sebastian

[Djork-Arné Clevert]

Hi Sebastian,

the KPGP-data is not phased, so it is probably not possible 

to infer the raw sequence from the vcf-file.

Like it or not, but for your purpose you have to use the sequence

alignment files, which are also available at www.camda.info.

Cheers,

Okko

-- 
Djork-Arné Clevert, PhD
Institute of Bioinformatics
Johannes Kepler University Linz

Phone: +49 30 4432 4702
Fax: +49 30 6883 5307
Email: ok...@clevert.de

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[Sebastian]

Dear Okko,

thanks for the hint! I wasn't aware of the problems that can occur when one ignores phasing.

I guess you talk about this BAM-file: https://www.wisconsingenomics.org/camda12/KPGP/KPGP1_G_110915_HiSeq_EastAsian_Kor_F.merge.bam.gz

Is there a standard pipeline documented somewhere that we could run on these BAM files to extract a raw sequence? I found something along the lines of:

samtools mpileup -uf reference.fa aligment.bam | bcftools view -cg - | vcfutils vcf2fq

Am I going in the right direction?

Sorry if these questions are trivial for you, but I have not much experience dealing with all these file different file formats.

Thanks,
Sebastian

[Djork-Arné Clevert]

Dear Sebastian, 

by gut feeling I would say you are heading for the right direction, 

but I instantly can't give you a reliable answer.  

However, I will try to gather extra information and come back to 

you asap.

Cheers,

Okko

  

-- 
Djork-Arné Clevert, PhD
Institute of Bioinformatics
Johannes Kepler University Linz

Phone: +49 30 4432 4702
Fax: +49 30 6883 5307
Email: ok...@clevert.de