java -jar GenomeAnalysisTK.jar -T ReadBackedPhasing -R reference.fasta -I reads.bam --variant SNPs.vcf -L SNPs.vcf -o phased_SNPs.vcf --phaseQualityThresh 20.0
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --variant  -V | NA | Input VCF file | |
| Optional Outputs | |||
| --out  -o | stdout | File to which variants should be written | |
| Optional Parameters | |||
| --cacheWindowSize  -cacheWindow | 20000 | The window size (in bases) to cache variant sites and their reads for the phasing procedure | |
| --maxGenomicDistanceForMNP Â -maxDistMNP | 1 | The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record | |
| --maxPhaseSites  -maxSites | 10 | The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm | |
| --min_base_quality_score  -mbq | 17 | Minimum base quality required to consider a base for phasing | |
| --min_mapping_quality_score  -mmq | 20 | Minimum read mapping quality required to consider a read for phasing | |
| --phaseQualityThresh  -phaseThresh | 20.0 | The minimum phasing quality score required to output phasing | |
| --sampleToPhase | NA | Only include these samples when phasing | |
| Optional Flags | |||
| --debug | false | If specified, print out very verbose debug information (if -l DEBUG is also specified) | |
| --enableMergePhasedSegregatingPolymorphismsToMNP Â -enableMergeToMNP | false | Merge consecutive phased sites into MNP records | |