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Old 09-06-2013, 06:43 AM   #1
jaavedm
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Location: United States

Join Date: Jun 2011
Posts: 8
Default Consensus fastq to VCF

Hello,

I'm looking for a tool to undo the vcf2fq operation performed by vcfutils.pl in the samtools package.

I have a bunch of consensus fastq D. melanogaster genomes obtained from the DPGP v2 project that were generated using vcf2fq (after aligning reads with BWA and calling 'samtools mpileup' to generate the initial vcf fiels):
http://www.dpgp.org/dpgp2/candidate/

My goal is to merge all these consensus fastq files and create one VCF file with all the SNPs across all fly lines. Using this "jumbo" VCF file, I'd like to eventually extract all the allele frequencies/counts per site of the genome. I will perform this aggregation by vcftools such as this:

Code:
vcftools --vcf jumbo.vcf --counts --out jumbo

Any ideas how to generate this jumbo.vcf file?

Thanks,
Jaaved
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