java -jar GenomeAnalysisTK.jar -T VariantsToBinaryPed -R reference.fasta -V variants.vcf -m metadata.fam -bed output.bed -bim output.bim -fam output.fam
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --metaData  -m | NA | Sample metadata file | |
| --variant  -V | NA | Input VCF file | |
| Required Outputs | |||
| --bed | NA | output bed file | |
| --bim | NA | output map file | |
| --fam | NA | output fam file | |
| Required Parameters | |||
| --minGenotypeQuality  -mgq | 0 | If genotype quality is lower than this value, output NO_CALL | |
| Optional Inputs | |||
| --dbsnp  -D | none | dbSNP file | |
| --outputMode  -mode | INDIVIDUAL_MAJOR | The output file mode (SNP major or individual major) | |
| Optional Flags | |||
| --checkAlternateAlleles | false | Checks that alternate alleles actually appear in samples, erroring out if they do not | |
| --majorAlleleFirst | false | Sets the major allele to be 'reference' for the bim file, rather than the ref allele | |