I am using GATK 4.0.12 and Picard 2.21.8. I don’t know what the difference between them is, all I know is that they have the same set of tools and that they both gave me the same error output.
I am trying to liftover an Altai Neanderthal genome from hg19 to hg38. I am using the following command :
java -jar picard.jar LiftoverVcf INPUT=AltaiNea.hg19_1000g.concat.vcf OUTPUT=AltaiNea.hg38_1000g.concat.vcf CHAIN=hg19ToHg38.over.chain R=hg38.fa REJECT=rejectedRecords.txt
and for some reason, the error message I am getting is:
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.IllegalArgumentException: Output format type is not set, or could not be inferred from the output path. If a path was used, does it have a valid VCF extension (.vcf, .vcf.gz, .bcf)? at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:462) at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:415) at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:355) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
I’m not sure why I’m getting this error. The input file is all 22 autosomal Neanderthal WGS vcfs concatenated with each other. The chain and the target reference are also correct. I unzipped all of the files for use with this program. Can I get some guidance? I’m not sure why it is telling me that the output format is incorrect.
Please sign in to leave a comment.