CombineVariants prioritize option
I have used CombineVariants to combine variants from GATK and samtools as shown below:
java -jar GenomeAnalysisTK.jar -T CombineVariants -R ref.fa --variant:GatkSNP GATKsnp.vcf --variant:GatkINDEL GATKind.vcf --variant:SamSNP Samsnp.vcf --variant:SamINDEL Samind.vcf -o allvar.vcf -genotypeMergeOptions PRIORITIZE -priority GatkSNP,GatkINDEL,SamSNP,SamINDEL --filteredrecordsmergetype KEEP_UNCONDITIONAL
This merges all the variants. However, with the above command, i do get the variants present in both GATK and samtools emitted from samtools.
I would like to get all the variants such that:
- variants present in both GATK and samtools emitted from GATK vcf files
- variants in only GATK
- variants in only samtools
could someone suggest any ideas or of there is something to be fixed in the command.