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# processing uncompressed VCFs via Picard?

LondonMember
edited June 2015

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

File vcfFile = new File("test2.vcf");

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

(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.

Tagged:

edited June 2015

@biogreen
Hi Martin,

I think Picard requires an index for any input vcf file. However, you can use GATK's Select Variants with -selectType to select out snps and indels. GATK will index the input file on the fly. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php#--selectTypeToInclude

-Sheila