Concatenate VCF files of non-overlapping genome intervals, all with the same set of samples
java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants -R reference.fasta -V input1.vcf -V input2.vcf -out output.vcf -assumeSorted
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --reference  -R | NA | genome reference file | |
| --variant  -V | NA | Input VCF file/s | |
| Required Outputs | |||
| --outputFile  -out | NA | output file | |
| Optional Outputs | |||
| --log_to_file  -log | NA | Set the logging location | |
| Optional Parameters | |||
| --logging_level  -l | INFO | Set the minimum level of logging | |
| --variant_index_parameter | -1 | the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator | |
| --variant_index_type | DYNAMIC_SEEK | which type of IndexCreator to use for VCF/BCF indices | |
| Optional Flags | |||
| --assumeSorted | false | assumeSorted should be true if the input files are already sorted (based on the position of the variants) | |
| --help  -h | false | Generate the help message | |
| --version | false | Output version information | |