parseSNP

[katholt]

No description provided.

[katholt]

coding consequences
tree post filtering

[d-j-e]

both coding consequences and tree post filtering (variation and conservation) restored/added to pipeline

[d-j-e]

parseSNPtable currently uses too much memory for larger files (e.g. 1.1 Gb allele table needs 80 Mb to be filtered!) - changing from dictionary to simpler 'string' structure for handling will reduce memory use to about 2X size of allele table (i.e about 2.2 Gb for the example above).

The full conversion is under way - will be included in next update of RedDog

Note: there is also a small error in the calculation of conservation filtering when outgroups are included - this will also be fixed in the updated version of parseSNPtable.

[d-j-e]

Full conversion of parseSNPTable.py now complete - now uses much less memory