Question: call sets resources to build indels recalibration model for maize (using GATK)
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gravatar for Medhat
23 months ago by
Medhat8.0k
Poland
Medhat8.0k wrote:

I am searching for data set to build indels recalibration model for maize using GATK, like java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R reference.fa -input recalibrated_snps_raw_indels.vcf -resource:mills,known=false,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.sites.vcf

in human they use Mills

Known and true sites training resource: Mills

searched in Panzea database the Maize HapMapV3.2.1 genotypes (with imputation by LinkImpute) they did not say that data contains indels as they declared before in Maize HapMapV2 genotypes

High quality genotypes were obtained for 55 million SNPs and small indels

more info from Panzea

any suggestions?

sequencing indels genome • 658 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by Medhat8.0k
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