I'm using the DRAGEN Enrichment analysis from Illumina's BaseSpace Sequence hub. In the input phase I set also the option Enable SV Calling (structural variants).
So, at the end of the analysis I obtain for each sample 2 vcfs: hard-filtered.vcf.gz and sv.vcf.gz. They have different size (5000kB vs 7kb usually) and obviously bring different information: I would like to merge them into a single vcf. What is the best tool that you could suggest me for this aim? For the same aim I merged 2 vcfs of the same sample from 3 different callers: haplotypecaller, freebayes and bso (Illumina BaseSpace on Cloud), using the tool of GATK CombineVariants. I report the example command:
java -jar /usr/local/cluster/bin/GenomeAnalysisTK.jar \ -T CombineVariants \ -R /storage/genomes/hg19/fa/hg19_masked.fa \ --variant:freebayes 19-3607_S10_FB.vcf.gz \ --variant:haplotype 19-3607_S10_HC.vcf.gz \ --variant:bso 19-3607_S1.vcf.gz \ -o merge_19-3607.vcf \ -genotypeMergeOptions PRIORITIZE \ -priority freebayes,haplotype,bso
As you can see in this example, I could define the type of the caller and also their prioritization during the merging: I would like to use a similar command defining two new type-caller, hard-filtered and sv, but when I tried I obtained a warning message, telling me that there aren't these caller inside the dictionary.
Can you help me to fix this problem? Have you ever meet this type of need with DRAGEN vcfs? Thanks for any help