VCFTools error: Unrecognized values used for CHROM, Replacing with 0.
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7.3 years ago

Hi all!

I was trying to run VCFtools on .vcf output file from dDocent program (http://ddocent.wordpress.com/) and I get this error:

Unrecognized values used for CHROM: E81_L257 -  Replacing with 0.

I was wondering if anyone encountered that and how it affects the data. Are there way to fix this?

 

Many thanks,

 

Irina

software error Assembly SNP • 3.5k views
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15 months ago
QPaps04 ▴ 80

Hello,

I know this is a very old post but I have just been trying to solve this exact problem. I have a genome that is made up of lots of scaffolds (not a model organism) and so I recieved the error message you report for all my scaffolds.

I found the solution by following this tutorial http://evomics.org/learning/population-and-speciation-genomics/2016-population-and-speciation-genomics/fileformats-vcftools-plink/ section 2.3.

To summarise you need to make your own chromosome map that vcftools uses to make the .ped format. Do this by running the following code:

  1. Create chromosome map

    bcftools view -H filename.vcf | cut -f 1 | uniq | awk '{print $0"\t"$0}' > filename.chrom-map.txt

  2. Make ped file using this chromosome map

    vcftools --vcf filename.vcf --plink --chrom-map filename.chrom-map.txt --out filename

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Very helpful! Thanks for posting!

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