MCHap

MCHap copied to clipboard

Currently there are a number of parameters that may be specified globally or on a per sample basis (using the global value as a default). This is a general pattern...

timothymillar

The VCF spec includes the option of having a CIGAR string for each alternate variant to describe how it aligns/differs from the reference allele. This would be an alternative the...

timothymillar

Depends on #72 When reducing haplotype-blocks to there constituent SNPs (#72), many SNPs will be redundant for the purpose of differentiating among the present haplotypes. It would be useful to...

timothymillar

Investigate supporting fixed-length MNP variants

1

Freebayes likes to output MNPs e.g. `TGC TAC,TGG`. Currently the best approach with these is to 'atomize' them into SNPs before assembly (removing redundant bases). There are two options to...

timothymillar

Currently this is done automatically but it should really be an option to turn on. If a duplicate SNP is encountered without this option enabled then an error should be...

timothymillar

From the spec `AF` is > Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes) So, it should be ok...

timothymillar