Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel truth sensitivity levels which were specified during VariantRecalibration
Using the tranche file generated by the previous step the ApplyRecalibration walker looks at each variant's VQSLOD value and decides which tranche it falls in. Variants in tranches that fall below the specified truth sensitivity filter level have their filter field annotated with its tranche level. This will result in a call set that simultaneously is filtered to the desired level but also has the information necessary to pull out more variants for a higher sensitivity but a slightly lower quality level.
The input raw variants to be recalibrated.
The recalibration table file in VCF format that was generated by the VariantRecalibrator walker.
The tranches file that was generated by the VariantRecalibrator walker.
A recalibrated VCF file in which each variant is annotated with its VQSLOD and filtered if the score is below the desired quality level.
java -Xmx3g -jar GenomeAnalysisTK.jar \ -T ApplyRecalibration \ -R reference/human_g1k_v37.fasta \ -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \ --ts_filter_level 99.0 \ -tranchesFile path/to/output.tranches \ -recalFile path/to/output.recal \ -mode SNP \ -o path/to/output.recalibrated.filtered.vcf
These Read Filters are automatically applied to the data by the Engine before processing by ApplyRecalibration.
This tool can be run in multi-threaded mode using this option.
This tool applies the following downsampling settings by default.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
|Argument name(s)||Default value||Summary|
||NA||The raw input variants to be recalibrated|
|NA||The input recal file used by ApplyRecalibration|
|NA||The input tranches file describing where to cut the data|
|NA||The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value|
|NA||If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file|
||NA||Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.|
|NA||Don't output filtered loci after applying the recalibration|
|NA||If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file.|
||NA||The VQSLOD score below which to start filtering|
||NA||The truth sensitivity level at which to start filtering|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Don't output filtered loci after applying the recalibration
If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file.
If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file
For this to work properly, the -ignoreFilter argument should also be applied to the VariantRecalibration command.
The raw input variants to be recalibrated
These calls should be unfiltered and annotated with the error covariates that are intended to use for modeling.
The VQSLOD score below which to start filtering
Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.
The --mode argument is an enumerated type (Mode), which can have one of the following values:
The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value
The input recal file used by ApplyRecalibration
The input tranches file describing where to cut the data
The truth sensitivity level at which to start filtering
GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA