Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

CatVariants does not combine header

rcholicrcholic DenverPosts: 63Member

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 \

After this, the combined_raw.snps_indels.vcf file only contains the header from raw.snps_indels-1.vcf, what might be wrong?

Best Answer

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