combinevariants after GATK 3.3 HC and UG calling
We do variant calling with UG (-glm SNPs) and HC (for both snps and indels) (gatk version 3.3) starting from the same sample.bam file.
At the end we would like to merge them in one .vcf.
- We would like to have just sample column, as if we we're dealing with just one sample.
- If the SNPs are called both with UG & HC, we would like to keep the exact variant line as it was present in the hc.vcf. So no recalculation of AC & DP values for example
- If the SNPs were only called with UG, we would like to keep the exact variant line as it was present in the ug.vcf
- for indels or snps that were only called with HC, we would like to keep the line as it was in hc. vcf
I've tried to accomplish this with CombineVariants using the following command:
java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg19_chr1-y.fasta -V:ug ug.vcf -V:hc hc.vcf --genotypemergeoption UNIQUIFY -o union.vcf
However when doing this we create a file with two sample columns one for ug & one for hc. And when the variant is present both in the ug.vcf and the hc.vcf the values in the INFO field are recalculated.
Is there a way to accomplish what we want using the CombineVariants tool?