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Multi-sample VCF generated in GATK is not working with novoutil IUPAC

Posted by sdarko on Thu 19 of July, 2012 21:54 MYT

Hi,

We are trying to find SNPs in a few loci of interest in rhesus macaque. To that end, we have sequenced exome sequences and I've gone through the process of calling SNPs using GATK and I've come up with a multi-sample VCF file.

Now we want to actually create alternative fasta references for each macaque at our loci of interest. I thought that Novocraft utility "novoutil iupac" would do exactly what I want it to do.

However, I'm receiving the following error:
"Loading VCF file...
novoutil: src/vcfsnps.cc:152: bool vcffile::hetero(tabbed&): Assertion `*gt == '|' || *gt == '/'' failed."

Any suggestions?

Thanks,
Sam Darko

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Posted by sdarko on Thu 19 of July, 2012 21:57 MYT

> Hi,
>
> We are trying to find SNPs in a few loci of interest in rhesus macaque. To that end, we have sequenced exome sequences and I've gone through the process of calling SNPs using GATK and I've come up with a multi-sample VCF file.
>
> Now we want to actually create alternative fasta references for each macaque at our loci of interest. I thought that Novocraft utility "novoutil iupac" would do exactly what I want it to do.
>
> However, I'm receiving the following error:
> "Loading VCF file...
> novoutil: src/vcfsnps.cc:152: bool vcffile::hetero(tabbed&): Assertion `*gt == '|' || *gt == '/'' failed."
>
> Any suggestions?
>
> Thanks,
> Sam Darko

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Posted by colin on Thu 19 of July, 2012 23:26 MYT

Hi,

VCF files vary a bit in their attributes. iupac is trying to check the zygosity of the SNP from the VCF file. It also assumes a single sample VCF file.

If you send us (support @ ...) part of the vcf file, say 10K lines, we'll fix it.

Best Regards, Colin

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Posted by colin on Mon 23 of July, 2012 16:34 MYT

Hi,

Next release will have support for multi-sample vcf files. This will allow application of SNPs from a specified sample or from all samples.

pre-Release is available on request

Colin

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