Tagged with #catvariants
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Comments (2)

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.

Comments (2)

Currently CatVariants -V only takes vcf/bcf files, I hope it can also take .list and vcf.gz files like other functions in GATK package.

Comments (3)

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 ?

Comments (1)

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?