I am using both GATK's UnifiedGenotyper and samtools mpileup as callers.
I've used CombineVariants in order to merge the two sets into a single .vcf file as follows:
java -Xmx4g -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta --variant:GATK GATK.vcf --variant:samtools samtools.vcf -o GATK_samtools.union.vcf -genotypeMergeOptions PRIORITIZE -priority GATK,samtools --filteredrecordsmergetype KEEP_UNCONDITIONAL
Now, I would like to select all calls that were called by both callers, regardless of whether they've been filtered or not.
From opening the GATK_samtools.union.vcf file, I understand that I need to select for the following expressions:
set=Intersection set=FilteredInAll set=filterInGATK-samtools
(I was also wondering why I don't get an expression like 'filterInsamtools-GATK'? does this have anything to do with the PRIORITIZE command?)
So... I've been trying to run the following with no luck (i.e. the output .vcf file doesn't contain any variants, but rather only the header):
java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta --variant GATK_samtools.union.vcf -select 'set == "Intersection"; -select 'set == "FilteredInAll";' -select 'set == "filterInGATK-samtools";' -o GATK_samtools.overlap.vcf
I've also tried the following, but in this case I only get the an output of the 'set=Intersection' variants, without the rest:
java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta --variant GATK_samtools.union.vcf -select 'set == 'Intersection';'FilteredInAll';'filterInGATK-samtools'" -o GATK_samtools.overlap.vcf
I'd appreciate any help on this.