Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
java -jar GenomeAnalysisTK.jar -T CombineGVCFs -R reference.fasta --variant sample1.g.vcf --variant sample2.g.vcf -o cohort.g.vcf
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --variant  -V | NA | One or more input gVCF files | |
| Optional Inputs | |||
| --dbsnp  -D | none | dbSNP file | |
| Optional Outputs | |||
| --out  -o | stdout | File to which the combined gVCF should be written | |
| Optional Parameters | |||
| --breakBandsAtMultiplesOf | 0 | If > 0, reference bands will be broken up at genomic positions that are multiples of this number | |
| --group  -G | [StandardAnnotation] | One or more classes/groups of annotations to apply to variant calls | |
| Optional Flags | |||
| --convertToBasePairResolution  -bpResolution | false | If specified, convert banded gVCFs to all-sites gVCFs | |
| Advanced Parameters | |||
| --annotation  -A | [AS_RMSMappingQuality] | One or more specific annotations to recompute. The single value 'none' removes the default annotations | |