CombineVariants set attribute filters on all callers explicitly (not with filteredInAll)

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jorgez

• September 01, 2020 11:41

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:

3.7-0-gcfedb67

b) Exact command used:

java -jar $EBROOTGATK/GenomeAnalysisTK.jar -T CombineVariants \
-R hg38.fa \
--variant:SAMTOOLS samtools.vcf \
--variant:PLATYPUS platypus.vcf \
--variant:VARSCAN varScan.vcf \
--variant:GATK gatk.vcf \
-o combined.vcf --genotypemergeoption UNSORTED

c) Entire error log:

There are no errors

If not an error, choose a category for your question(REQUIRED):
b) What does (......) mean?
I have succesfully run CombineVariants to combine four VCF files, each from a different variant caller.

For a particular variant I see the set attribute as:

set=filterInPLATYPUS-SAMTOOLS-VARSCAN-GATK

I understand that particular variant was filtered out (not a PASS) in some way in the four variant callers. However in such case I would expect the set attribute to be:

set=filteredInAll

My question is. What is the difference between set=filterInPLATYPUS-SAMTOOLS-VARSCAN-GATK and set=filteredInAll ?

Thanks so much,

Jorge

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• 

  Genevieve Brandt (she/her)

  • September 01, 2020 21:29

  Hello jorgez, our GATK support team does not support GATK 3 anymore. We recommend using GATK4 because of the many improvements! See this link for getting started.

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