Question: about GATK VariantAnnotator and VCF files
1
gravatar for Bogdan
2.9 years ago by
Bogdan720
Palo Alto, CA, USA
Bogdan720 wrote:

Dear all,

talking about VariantAnnotator in GATK : https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php, please could you advise :

could it be safely used on VCF files produced by other callers like STRELKA, VIRMID, Varscan2 etc ...beside MUTECT1 or MUTECT2 ? I am referring to the use of VariantAnnotator with the options for FS, SOR, RMSMappingQuality, QualByDepth, ReadPosRankSumTest ...

or, are there any minimal requirements for a VCF file produced by other somatic mutation callers in order to be fully annotated by VariantAnnotator ?

thank you,

-- bogdan

vcf • 1.5k views
ADD COMMENTlink modified 2.9 years ago by Sean Davis25k • written 2.9 years ago by Bogdan720
0
gravatar for Sean Davis
2.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

GATK VariantAnnotator can be used for VCFs from somatic variant callers as well.

ADD COMMENTlink written 2.9 years ago by Sean Davis25k
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