This is a test version of Biostars. For the public version, visit https://www.biostars.org.
variant Recalibrator, -an option

Hello!

I would like to understand the -an option in Variant Recalibrator of GATK. (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php)

For example, If I use the -an DP option, what will GATK do?

Thank you in advance

gatk variant recalibrator -an
• 1,673 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by noeD noeD

1 answer

the an is a set of annotations that will be used from the VCF to "learn' what is a good/bad variant.

for example if a majority of the "bad" variants have DP<20 and the "good" have DP>=20, this model will be used to take a decision.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this
  • How to build my resource-bundle for variant recalibrator?
    written by Sakhaa • Sakhaa
    Hello everyone, I have a specific data set and I want to use it as resource bundle to train my model. Could anyone guides me …
  • GATK GetSampleName is not working?
    written by imanthony1993 • imanthony1993
    Hi. Recently I am running a tumor-only SNV calling pipeline and encounter a problem when running GATK GetSampleName. In the tutorial (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_GetSampleName.php), the code is …
  • GATK -Xmx4G and -Xmx8G
    written by lovegenetics • lovegenetics
    Dear all, I would like to know what the difference is between the "-Xmx4G" and "-Xmx8G" switches on GATK. All I know is, both of …
  • gatk HaplotypeCaller options
    written by maricom • maricom
    Hi, I am counting variants using gatk HaplotypeCaller, however, I am not sure the difference between two options, MappingQualityReadFilter and MappingQualityFilter. I read the documents, …
  • how to run GATK CalculateGenotypePosteriors on a case-control cohort
    written by blueskypie • blueskypie
    One usage [example][1] is to refine genotypes based on the discovered allele frequency in an input VCF containing many samples ``` gatk CalculateGenotypePosteriors -V multisample_input.vcf.gz …
  • samtools mpileup keeps making an empty file
    written by James Reeve James Reeve
    I'm trying to call SNPs from a pooled DNA sample using the [PoPoolation2 pipeline][1]. I'm stuck on a step that requires me to make a …
  • dbsnp hg 38
    written by noeD noeD
    Hello! I am using `GATK -T BaseRecalibrator` in my pipeline for whole exon sequencing, and I would like to indicate the -knownSites option, therefore I …
  • featuresCount order sam file?
    written by noeD noeD
    Hello! I am using featuresCount for read summarization, with the following command: featureCounts -T 5 -t exon -g gene_name -a genomehg38.gtf -o counts.txt file.sam I …
  • dbsnp file for C. elegans
    written by biomagician biomagician
    Hi, I want to use this tool here from GATK: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_varianteval_VariantEval.php VariantEval It has the optional option to input a dbsnp file --dbsnp. Does anybody …
  • CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
    written by William William
    Does CombineGVCFs + GenotypeGVCFs software exist for gVCF files produced by Freebayes? Since December 2015 Freebayes support gVCF files as output: https://github.com/ekg/freebayes/releases/tag/v1.0.2 It's now more …