snp-sites
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sanger-pathogens
Output invariant sites and nucleotide frequencies
In general, phylogenetic programs use invariant sites for likelihood calculations. However, a number of programs, such as RAxML and BEAST, can perform ascertainment bias corrections given the number of invariant sites and the frequencies of nucleotides in the alignment. If SNP-sites output these values, they could be used as direct inputs for RAxML, for example.
I second this suggestion.
Either add a -s (stats?) option to report all sorts of columnar statistics, characters used etc.
OR
Always output this to stderr as part of the logs.
Grand, give me a toy example and I'll sort it out
On 27 September 2017 at 08:53, Torsten Seemann [email protected] wrote:
I second this suggestion.
Either add a -s (stats?) option to report all sorts of columnar statistics, characters used etc.
OR
Always output this to stderr as part of the logs.
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From your example in the README:
sample1 AGACACAGTCAC sample2 AGACAC----AC sample3 AAACGCATTCAN
-s (or stderr) would produce:
Input stats: Alignment length: 12 Proportion Ns: 0.03 Proportion Gap sites: 0.11 Nucleotide frequencies (A,G,C,T): 45.2,12.9,32.3,9.7
Output stats: SNP alignment length: 3 Number Gap sites (-) introduced: 1 Proportion gap sites: 0.11
Thinking about this more, I obviously came up with a couple other useful stats. seqtk comp can produce similar stats, but having them in one tool with the speed of SNP-sites would be great.
