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# Using SelectVariants to select for multiple expressions

Member

Hi,

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.

Thanks!

Sagi

Tagged:

Hi Sagi,

Have you looked at some records inside your combined variants file to check that the sets were annotated correctly?

• Member

Hi Geraldine,

Yes of course. The annotations are fine.

A little confused I must say... Any ideas?

Thanks!

Sagi

Hi Sagi,

Sorry for not getting back to you earlier. Th only thing I can think of is, have you tried selecting on a single set at a time?

• Member

Hi Geraldine,

The idea is to select for all shared variants across both cal sets... I don;t really see how I can do this without using CombineVariants and then SelectVariants...?

Thanks!

Sagi

I meant try to select eg the Intersection set and see if that works. If it does then you can move on to getting all of them; but first you want to make sure the tool is working properly on one set. This is to distinguish syntax issues from other problems.

• Member

Hi Geraldine,

Yes it indeed works. How can I select for multiple expression at once?

Thanks!

Sagi