533
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
Major updates.
Major updates.
1. More flexible loading functions for VCF files.
1. Update the algorithm to allow nuclear and multi-generational pedigrees
2.
2. Add a feature to use reference panel
3.
3. More flexible loading functions for VCF files (no need to remove non-SNP variant).
Shotgun Sequences: --vcf [], --pedfile []
Shotgun Sequences: --vcf [], --pedfile []
Markov Sampler: --seed [], --burnin [], --rounds []
Markov Sampler: --seed [], --burnin [], --rounds []
Haplotyper: --states [], --errorRate [], --compact
Haplotyper: --states [], --errorRate []
Phasing: --randomPhase , --inputPhased, --refPhased
Phasing: --randomPhase , --inputPhased, --refPhased
Output Files: --prefix [], --phase, --interimInterval []
Output Files: --prefix [], --phase, --interimInterval []
To complete our example analysis, we could run:
To complete our example analysis, we could run:
FamLDCaller --vcf result/chr20.mpileup.vcf --pedfile ped/triocaller.ped --states 50 --rounds 10 --prefix result/chr20.triocaller
FamLDCaller --vcf test.vcf --pedfile test.ped --states 50 --rounds 10 --prefix test.famldcaller
