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# processing uncompressed VCFs via Picard?

LondonMember Posts: 4
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");
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.

Tagged:

## Answers

• Broad InstituteMember, Broadie, Moderator Posts: 4,702 admin
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

• Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin

Hi @biogreen, are you trying to develop a tool using Picard as a library? I'm afraid we currently don't provide support for that kind of usage. My recommendation is to make sure you use an IDE like IntelliJ, which will provide syntax highlighting and code completion suggestions. Those are very helpful for debugging Java code, if you're not already using them.

Geraldine Van der Auwera, PhD

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