If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:
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:
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:
My question is. What is the difference between set=filterInPLATYPUS-SAMTOOLS-VARSCAN-GATK and set=filteredInAll ?
Thanks so much,
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