Problem GATK with CountCovariates

[amathieu]

Hello,

I use GATK v1.2-4-gd9ea764 and when i use this command :

java -Xmx4G -jar GenomeAnalysisTK/GenomeAnalysisTK.jar -l INFO -R chr7.fa -I seq.bam --DBSNP snp132.txt -T CountCovariates -cov ReadGroupConvariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile seq.recal_data.csv


I have this message :

MESSAGE: Argument with name 'DBSNP' isn't defined.

Then I use different argument but none work. Have you an idea ?

Thank

[Bukowski]

You specify dbSNP (in vcf format) like this:

-B:dbSNP,VCF /your/dbsnp.vcf

[amathieu]

When I specify -B:dbsnp,vcf 00-All.vcf

I have this message : Invalid command line: The parameter rodBind is deprecated. Bindings for reference-ordered data, in the form :<name>,<type> <file>

[Bukowski]

When I specify -B:dbsnp,vcf 00-All.vcf

I have this message : Invalid command line: The parameter rodBind is deprecated. Bindings for reference-ordered data, in the form :<name>,<type> <file>

I may be wrong but I'm pretty sure the VCF needs to be capitalised. I'm not using that version of GATK however.

[amathieu]

Always the same problem.

[Bukowski]

Always the same problem.

OK, the behaviour has certainly changed in 1.2

Try this:

java -jar -Xmx8G GenomeAnalysisTK.jar -l INFO -T CountCovariates -R your_reference.fasta -knownSites:dbsnp,VCF yourdbsnp.vcf -knownSites:indels,VCF yourindels.vcf -I input.bam -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile covariate_table.csv

(or local equivalents)

[sehrrot]

OK, the behaviour has certainly changed in 1.2

Try this:

java -jar -Xmx8G GenomeAnalysisTK.jar -l INFO -T CountCovariates -R your_reference.fasta -knownSites:dbsnp,VCF yourdbsnp.vcf -knownSites:indels,VCF yourindels.vcf -I input.bam -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile covariate_table.csv

(or local equivalents)

Hi Bukowski

where can I yourindel.vcf for download knownSites:indels? Is it all included in dbsnp135 vcf file?

[Bukowski]

Hi Bukowski

where can I yourindel.vcf for download knownSites:indels? Is it all included in dbsnp135 vcf file?

Try the GATK resource bundle:

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