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PlantandFoodResearch
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MCHap
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
MIT License
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Consider replacing `ADMF` with `AF` in find-snvs output
#183
timothymillar
opened
2 months ago
0
Sparse representation of genotype posterior
#182
timothymillar
opened
3 months ago
1
Add call-pedigree branch to CI testing
#181
timothymillar
closed
3 months ago
0
Update setup.py
#180
rfinkers
closed
3 months ago
0
version
#179
rfinkers
opened
3 months ago
1
Version 0.9.3
#178
timothymillar
closed
4 months ago
0
Improve error messages for mismatching Reference/VCF/BAM
#177
timothymillar
closed
4 months ago
0
Correct usage of `AN` field
#176
timothymillar
closed
4 months ago
0
Version 0.9.2
#175
timothymillar
closed
4 months ago
0
Additional info fields
#174
timothymillar
opened
4 months ago
0
Avoid holding alignment file handles open.
#173
timothymillar
closed
4 months ago
1
Improve defaults for find-snvs
#172
timothymillar
closed
4 months ago
1
Allow setting of precision for floats in VCF
#171
timothymillar
opened
4 months ago
0
Version 0.9.1
#170
timothymillar
closed
7 months ago
0
Version 0.9.0
#169
timothymillar
closed
8 months ago
0
Replace `--skip-rare-haplotypes` with a generic `--filter-haplotypes` argument.
#168
timothymillar
closed
8 months ago
2
Improve CRAM performance by passing reference fasta
#167
timothymillar
closed
8 months ago
1
Script to generate template VCF file for assembly
#166
timothymillar
closed
8 months ago
2
Allow masking of SNV reference alleles
#165
timothymillar
opened
1 year ago
0
Allow multiple readgroups for a single sample
#164
timothymillar
closed
8 months ago
1
Improve error messages for uncompressed and non-indexed input files.
#163
sjclare
closed
4 months ago
3
Report posterior probability of allele presence
#162
timothymillar
closed
8 months ago
1
Filtering options or tool
#161
timothymillar
opened
1 year ago
1
Table with likelihood of membership of a read in an allele
#160
rfinkers
opened
1 year ago
1
Add Dockerfile
#159
timothymillar
closed
1 year ago
0
Fix integer overflow and bump to version 0.8.1
#158
timothymillar
closed
1 year ago
0
Avoid integer overflow when calculating unique number of haplotypes
#157
timothymillar
closed
1 year ago
0
Dockerfile
#156
timothymillar
closed
1 year ago
1
Option to drop uncalled haplotypes
#155
timothymillar
opened
1 year ago
1
Simplify prior allele freqs specification
#154
timothymillar
closed
8 months ago
2
Report population AFP by default
#153
timothymillar
opened
1 year ago
0
Example notebook
#152
timothymillar
closed
1 year ago
0
Version 0.8.0
#151
timothymillar
closed
1 year ago
0
Add 1 to specified cores number when making thread pool
#150
timothymillar
closed
8 months ago
1
Simplify input parameters
#149
timothymillar
closed
1 year ago
0
Add version command
#148
timothymillar
closed
1 year ago
0
Improve handeling of allele priors and reference allele
#147
timothymillar
closed
1 year ago
0
Indicate when the reference allele is reported only as a requirement of the VCF format
#146
timothymillar
closed
1 year ago
3
Handle edge-case where all prior allele frequencies are zero
#145
timothymillar
closed
1 year ago
2
Remove outated section from README.md
#144
timothymillar
closed
2 years ago
0
Version 0.6.0
#143
timothymillar
closed
2 years ago
0
Population prior allele frequencies
#142
timothymillar
closed
2 years ago
0
Tidy CLI and and remove KMERCOV
#141
timothymillar
closed
2 years ago
0
F/sample pooling
#140
timothymillar
closed
2 years ago
0
Consider defaulting flat prior across genotypes
#139
timothymillar
opened
2 years ago
0
Remove pedigraph tool and simplify requirements
#138
timothymillar
closed
2 years ago
0
Beter default parameters
#137
timothymillar
closed
2 years ago
1
Posterior mean dosage 'DS'
#136
timothymillar
opened
2 years ago
0
F/103 posterior allele frequency
#135
timothymillar
closed
2 years ago
0
Remove KMERCOV
#134
timothymillar
closed
2 years ago
1
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