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Download here. Version.
A general guideline for genotyping calling in families.
Polymutt: Small to big pedigrees, modest to high depth
FamLDCaller: many small pedigrees, low to modest depths.
FamLDCaller is an extension of [http://genome.sph.umich.edu/wiki/TrioCaller TrioCaller] to handle nuclear and general family structure.
'''Download''':
[[Binary file:]] [http://www.pitt.edu/~wec47/Files/FamLDCaller FamLDCaller]. [Last update: 08/15/2014]
More details will come soon. Please contact Wei Chen at weichen.mich@gmail.com for any questions.
Major updates.
Major updates.
1. More flexible loading functions for VCF files.
1. Update the algorithm to allow nuclear and multi-generational pedigrees
2. Add a feature to use reference panel
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 test.vcf --pedfile test.ped --states 50 --rounds 10 --prefix test.famldcaller
