Apply a score cutoff to filter variants based on a recalibration table
java -jar GenomeAnalysisTK.jar -T ApplyRecalibration -R reference.fasta -input raw_variants.vcf --ts_filter_level 99.0 -tranchesFile output.tranches -recalFile output.recal -mode SNP -o path/to/output.recalibrated.filtered.vcf
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --input | NA | The raw input variants to be recalibrated | |
| --recal_file  -recalFile | NA | The input recal file used by ApplyRecalibration | |
| Optional Inputs | |||
| --tranches_file  -tranchesFile | NA | The input tranches file describing where to cut the data | |
| Optional Outputs | |||
| --out  -o | stdout | The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value | |
| Optional Parameters | |||
| --ignore_filter  -ignoreFilter | NA | If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file | |
| --mode | SNP | 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. | |
| --ts_filter_level | NA | The truth sensitivity level at which to start filtering | |
| Optional Flags | |||
| --excludeFiltered  -ef | false | Don't output filtered loci after applying the recalibration | |
| --ignore_all_filters  -ignoreAllFilters | false | If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file. | |
| --useAlleleSpecificAnnotations  -AS | false | If specified, the tool will attempt to apply a filter to each allele based on the input tranches and allele-specific .recal file. | |
| Advanced Parameters | |||
| --lodCutoff | NA | The VQSLOD score below which to start filtering | |