Need help converting VCF 4.1 file to 4.0

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8.9 years ago

idedios ▴ 30

So today I learned Illumina's VariantStudio 2.2.1 does not accept VCF v4.1 files. I was told I could convert them to the older 4.0 format but I'm not sure how to best go about doing that.

Attached is the error message from importing the troubled VCF file.

screenshot of error message

next-gen • 2.7k views

ADD COMMENT • link updated 15 months ago by Ram 43k • written 8.9 years ago by idedios ▴ 30

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Do you know if it accepts gzipped file?

ADD REPLY • link updated 15 months ago by Ram 43k • written 8.9 years ago by arnstrm ★ 1.8k

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I know it does. When I try loading the unzipped version it just says "Invalid input string".

Also I tried bgzipping and tabix-ing it but it didn't change anything.

ADD REPLY • link updated 15 months ago by Ram 43k • written 8.9 years ago by idedios ▴ 30

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So I've made some progress by using vcftools vcf-convert script however it appears a lot of data from the original file is now missing. The filesize of the original vcf was 254MB but now the converted vcf is only 14MB in size. Even the original vcf.gz was 34MB in size.

At least I can import the data into variantstudio now.

ADD REPLY • link updated 15 months ago by Ram 43k • written 8.9 years ago by idedios ▴ 30

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