Tagged with #filtervariants
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Created 2015-08-31 10:15:59 | Updated | Tags: picard filtervariants
Comments (8)

Dear all, I have a problem using Picard tool FilterVcf. I first run the command:

java -jar picard.jar FilterVcf \ MIN_AB=10.0 \ INPUT=12-3455_S6.final.vcf \ OUTPUT=test.vcf

And I receive the error:

[Mon Aug 31 12:04:53 CEST 2015] Executing as smerella@b002 on Linux 2.6.32-279.2.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18; Picard version: 1.138() JdkDeflater [Mon Aug 31 12:04:56 CEST 2015] picard.vcf.filter.FilterVcf done. Elapsed time: 0.06 minutes. Runtime.totalMemory()=1138753536 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.IllegalArgumentException: A reference dictionary is required for creating Tribble indices on the fly at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:389) at picard.vcf.filter.FilterVcf.doWork(FilterVcf.java:97) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

Then I tried with: java -jar picard.jar FilterVcf \ REFERENCE_SEQUENCE=/lustre1/genomes/hg19/fa/hg19 \ MIN_AB=10.0 \ INPUT=12-3455_S6.final.vcf \ OUTPUT=test.vcf

And I received the same error. In the directory /lustre1/genomes/hg19/fa/ I have the files hg19.dict hg19.fa hg19.fa.fai. I don't understand what I am doing wrong.

Thanks for the help.

[smerella@b002 scratch_bmc]$ java -jar picard.jar FilterVcf --version 1.138()


Created 2013-10-30 18:51:30 | Updated | Tags: selectvariants vcf filtervariants
Comments (3)

Hi Team, I have a VCF which I'd like to filter by variant frequency. The problem is, my frequencies are percentages rather than decimals. Is there a workaround in JEXL which allows it to parse the '%' operator as a percentage (or ignore it entirely) rather than considering the field a string upon seeing the modulo operator? The VCF also has two columns in the format column (a normal and a tumor). Is it possible to drill down into these using just the genotypeFilterExpression/genotypeFilterName flags or must do something else?

Thanks, Eric T Dawson