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processing uncompressed VCFs via Picard?

biogreenbiogreen LondonMember Posts: 4
edited June 2015 in Ask the GATK team

I am trying to open small uncompressed VCFs via picard-tools-1.119, via SplitVcfs.jar.

File vcfFile = new File("test2.vcf");
VCFFileReader vcfReader = new VCFFileReader(vcfFile,false);

Even though I've specified that an index is not required in the constructor, this generates the following error:

htsjdk.tribble.TribbleException: Index not found for: MYLOCATION\test2.vcf
at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:253)
at htsjdk.variant.vcf.VCFFileReader.query(VCFFileReader.java:124)

(if I don't specify the index parameter, then it generates a different error:"An index is required, but none found" )

I've attached a test file so you can see it for yourself. ( NOTE: I've had to compress it into a .zip, otherwise the forum didn't allow me to attach the file itself, but if you want to replicate my results you will need to uncompress it and try loading the plain file (test2.vcf).

My question: is there any way to open uncompressed VCF files in picard via VCFFileReader or otherwise?

Thanks
Martin

PS: these are small VCFs that would be exported out from larger datasets, so compressing/indexing them would seem like an unnecessary extra step.

zip
zip
test2.zip
2K

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