PlantandFoodResearch/MCHap

Issues

• Consider replacing `ADMF` with `AF` in find-snvs output

  #183 opened 6 months ago by timothymillar
  0

• version

  #179 opened 8 months ago by rfinkers
  1

• Sparse representation of genotype posterior

  #182 opened 7 months ago by timothymillar
  1

• Additional info fields

  #174 opened 9 months ago by timothymillar
  0

• Improve defaults for find-snvs

  #172 opened 8 months ago by timothymillar
  1

• Improve error messages for uncompressed and non-indexed input files.

  #163 opened 8 months ago by sjclare
  3

• Correct usage of `AN` field

  #176 opened 8 months ago by timothymillar
  0

• Improve error messages for mismatching Reference/VCF/BAM

  #177 opened 8 months ago by timothymillar
  0

• Avoid holding alignment file handles open.

  #173 opened 8 months ago by timothymillar
  1

• Allow setting of precision for floats in VCF

  #171 opened 9 months ago by timothymillar
  0

• Allow masking of SNV reference alleles

  #165 opened a year ago by timothymillar
  0

• Documentation

  #121 opened 3 years ago by timothymillar
  4

• Replace `--skip-rare-haplotypes` with a generic `--filter-haplotypes` argument.

  #168 opened a year ago by timothymillar
  2

• Improve CRAM performance by passing reference fasta

  #167 opened a year ago by timothymillar
  1

• Simplify prior allele freqs specification

  #154 opened a year ago by timothymillar
  2

• Report posterior probability of allele presence

  #162 opened a year ago by timothymillar
  1

• Add 1 to specified cores number when making thread pool

  #150 opened a year ago by timothymillar
  1

• Script to generate template VCF file for assembly

  #166 opened a year ago by timothymillar
  2

• Allow multiple readgroups for a single sample

  #164 opened a year ago by timothymillar
  1

• Option to drop uncalled haplotypes

  #155 opened 2 years ago by timothymillar
  1

• Dockerfile

  #156 opened a year ago by timothymillar
  1

• Filtering options or tool

  #161 opened 2 years ago by timothymillar
  1

• Table with likelihood of membership of a read in an allele

  #160 opened 2 years ago by rfinkers
  1

• Avoid integer overflow when calculating unique number of haplotypes

  #157 opened 2 years ago by timothymillar
  0

• Report population AFP by default

  #153 opened 2 years ago by timothymillar
  0

• Document an example workflow for calling haplotypes in a mapping population

  #123 opened 2 years ago by timothymillar
  0

• Simplify input parameters

  #128 opened 2 years ago by timothymillar
  1

• Handle edge-case where all prior allele frequencies are zero

  #145 opened 2 years ago by timothymillar
  2

• Indicate when the reference allele is reported only as a requirement of the VCF format

  #146 opened 2 years ago by timothymillar
  3

• Consider defaulting flat prior across genotypes

  #139 opened 2 years ago by timothymillar
  0

• Temperature gradiaent for parallel-temporing

  #126 opened 3 years ago by timothymillar
  0

• Allow specification of population prior allele frequencies with mchap call

  #120 opened 2 years ago by timothymillar
  1

• Drop zero-count alleles

  #113 opened 2 years ago by timothymillar
  3

• Beter default parameters

  #137 opened 2 years ago by timothymillar
  1

• Remove KMERCOV

  #134 opened 2 years ago by timothymillar
  1

• Remove pedigraph tool and simplify requirements

  #138 opened 2 years ago by timothymillar
  0

• Low memory version of exact calling method returns incorrect posterior mode probability

  #133 opened 3 years ago by timothymillar
  1

• Posterior mean dosage 'DS'

  #136 opened 3 years ago by timothymillar
  0

• Default to constant base error rate

  #127 opened 3 years ago by timothymillar
  0

• Test against newer Python version

  #122 opened 3 years ago by timothymillar
  1

• Simplify PMF for calling Gibbs sampler

  #125 opened 3 years ago by timothymillar
  1

• Remove use of factorial in prior probability function

  #124 opened 3 years ago by timothymillar
  0

• Final alt allele count includeds counts of null allleles

  #115 opened 3 years ago by timothymillar
  1

• Integer overflow caused by use of in8 for alleles in greedy_caller

  #117 opened 3 years ago by timothymillar
  1

• Option to use previous call as initial genotype when re-calling

  #116 opened 3 years ago by timothymillar
  0

• Unifiy posterior mode methods

  #114 opened 3 years ago by timothymillar
  0

• Seperate haplotype assembly and re-calling into two seperate tools.

  #110 opened 3 years ago by timothymillar
  1

• Unify exact calling methods

  #111 opened 3 years ago by timothymillar
  0

• Generalise default and per sample specification of parameters

  #107 opened 3 years ago by timothymillar
  0

• Add CIGAR string for variants.

  #105 opened 3 years ago by timothymillar
  0