The current GATK version is 3.5-0

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# CatVariants does not combine header

DenverPosts: 68Member

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?

Tagged:

• Posts: 8Member

A related issue I had was that when I was trying to concatenate two VCFs from the same sample, one containing the (filtered) variants and one with non-variants, I got an error saying that the FS filter field wasn't in the header. This was because I had set the non-filtered VCF as first input, making the script take the header from that file, which of course didn't have a FS filter field (because no VariantFiltration had been run on it). It was easily solved by just reversing the input ordering, making the script take the most complete header available. Just an FYI if somebody else runs into a similar problem!