| allelicDepth |
Writing genotype likelihoods to a GLF file |
| bed |
Join bed files: region + mask, union or intersect |
| call |
Calling genotypes |
| createMask |
Creating a mask BED file |
| DStat |
ABBA-BABA statistic |
| estimateErrors |
Estimating PMD pattern and Sequencing Errors |
| GLF |
Writing genotype likelihoods to a GLF file |
| mutationLoad |
Estimating mutation load across the genome |
| pileup |
Printing pileup from BAM file |
| pileupToBed |
Create bed file from pileup file |
| PSMC |
Generating a PSMC Input file probabilistically |
| summaryStats |
Summary statistics per window/genomewide: Felsenstein, HKY85, Pi |
| thetaRatio |
Estimate ratio in heterozygosity (theta) between genomic regions |