MCHap

MCHap copied to clipboard

Sparse representation of genotype posterior

1

Investigate a sparse encoding of genotype posteriors. E.g. an equivalent to the `PP` field (phred-scaled probabilities) in which zeoro values are omitted. This can be represented as a map of...

timothymillar

Some additional (optional) info fields that would speed up filtering etc. - `MCIP`/`MCIT`: proportion/count of samples found with evidence of Markov chain incongruence - `SAFP`: sum of posterior allele frequencies...

timothymillar

version

1

-v and/or --version to print the mchap version (information)

rfinkers

Current default is 3dp. This isn't enough in some circumstances.

timothymillar

Reusing the `REFMASKED` flag, allow masking of the reference allele of a SNV in MCHap assemble. This avoids unnecessarily treating a biallelic SNV as triallelic due to the refence genome...

timothymillar

Documentation

4

Need to write some more extensive documentation. - [x] General background - [x] How tools fit together `assemble`, `call` etc. - [ ] Use of more advanced features such as...

timothymillar

Option to drop uncalled haplotypes

1

MCHap can report haplotypes that have not been called in the posterior mode of any individual (i.e., and allele count of 0). This is necessary when reporting statistics over the...

timothymillar

Filtering options or tool

1

Consider options or separate tool for filtering based on reported metrics. *Add filtering options to existing tools:* - Simpler as less double handling of values - Adds additional complexity to...

timothymillar

Table with likelihood of membership of a read in an allele

1

Would it be possible to write a table, for each locus, in which the likelihood that a read belongs to an allele is reported?

rfinkers

this isn't too big and is very useful

timothymillar