Using GATK on command-line the CatVariants command fails.
Program version: GATK 3.1-1-g07a4bf8.
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: CatVariants
Code to invoke:
java -jar GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -T CatVariant -R file.fasta
Note that in the current documentation for CatVariants the example lists the name as 'org.broadinstitute.sting.tools.CatVariants' rather than just CatVariants. Trying the listed string fails with the same error.
If I want to merge different VCF files, which I used -L argument for calling variants against to different chromosomes individually with the same list of samples by HaplotypeCaller. I mean the sample are the same, I just used -L to call variants chromosome by chromosome separately. I suppose whether catVariants or CombineVariant will give me the same results, right ?
Below is the command:
java -cp $CLASSPATH/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \ -R GATK_ref/hg19.fasta \ -V ../GATK/VQSR/parallel_batch/raw.snps_indels-1.vcf \ -V ../GATK/VQSR/parallel_batch/raw.snps_indels-2.vcf \ -V ../GATK/VQSR/parallel_batch/raw.snps_indels-3.vcf \ -out ../GATK/VQSR/parallel_batch/combined_raw.snps_indels.vcf \ -log ../GATK/VQSR/parallel_batch/log/combined.log \ -assumeSorted
After this, the combined_raw.snps_indels.vcf file only contains the header from raw.snps_indels-1.vcf, what might be wrong?