Tablerecalibration

Question

[Peyman]

I use GATK and when i use this command :

java -jar GenomeAnalysisTK.jar -T TableRecalibration -R ucsc.hg19.fasta -I /reorder_rg_realign_rmdup_cl.bam -L SureSelect_All_Exon_50mb_with_annotation_hg19.bed --knownSites:dbsnp,VCF dbsnp_132.hg19.vcf --knownSites:indels,VCF 1000G_biallelic.indels.hg19.vcf -o outmerge_reorder_rg_realign_rmdup_cl_recal.bam -recalFile /recal_data_cl.csv -l INFO

I have this message :

MESSAGE: Argument with name 'knownSites' isn't defined

Then I use different argument but none works e.g. -B: and --known. Have you an idea ?

Peyman

Answer 1

[David Quigley]

java -jar GenomeAnalysisTK.jar -T TableRecalibration --help

TableRecalibration does not have an argument called knownSites.

[User 59]

I don't think it supports -B rod bindings either for that matter

Answer 2

[Brad Chapman]

To expand on David's answer, the documentation on the GATK is worth reading to get an overview of the two-step recalibration process:

http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration

First run CountCovariates, which has the '-knownSites' argument you are looking for:

CountCovariates command line documentation

As Daniel mentioned, the 'rod' style syntax is no longer supported as of GATK 1.2, the latest release.

After CountCovariates, then you run TableRecalibration with the recalibration file produced. You don't need to specify knownSites again:

TableRecalibration command line documentation

[David Quigley]

Thanks for a more thoughtful and complete answer than mine.