VariantRecalibrator in GATK

Question

[897598644]

Excuse me:

I used unifiedGenotyper in GATK to call variants and filterd variants with VQSR. There were errors:

java -jar GenomeAnalysisTK.jar \ 
    -T ApplyRecalibration \ 
    -R reference.fa \ 
    -input raw_variants.vcf \ 
    -mode SNP \ 
    --ts_filter_level 99.0 \ 
    -recalFile recalibrate_SNP.recal \ 
    -tranchesFile recalibrate_SNP.tranches \ 
    -o recalibrated_snps_raw_indels.vcf

The log said

##### ERROR MESSAGE: Argument with name '--resource' (-resource) is missing.
##### ERROR Argument with name '--use_annotation' (-an) is missing.

Was the error in UnifiedGenotyper? When I used HaplotypeCaller, it did not print out error.

Any thing that helped me understand the issue would be much appreciated.

[897598644]

I have found the error.

Thanks again.

[karl.stamm]

This is not an answer to the original question, and it carries no information for other's who come upon this question.

For the benefit of the community, you must tell us what you found, or fixed.

[897598644]

Thanks to Karl's suggestion. It was the path error that I did not find.

Answer 1

[Brice Sarver]

You need to specify the truth and training datasets, as well as the annotations, when you run VariantRecalibrator. You build the model under your set of criteria and then apply it to your dataset.

For more help, check out this GATK guide.