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Ancestral Sequence
Skylar Wyant edited this page May 20, 2016
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Convert a BAM file to a fasta file using ANGSD. Please see ANGSD's tutorial page for full details on this method.
To run this method, use the following command
angsd-wrapper Ancestral Ancestral_Sequence_Config
where Ancestral_Sequence_Config
is the full path to the configuration file for the 2D site frequency spectrum and Fst estimations.
All inputs should be specified in Ancestral_Sequence_Config
.
This method does not make use of Common_Config
.
This variable is specific to this method:
Variable | Function |
---|---|
ANC_BAM |
The full path to the BAM file to be converted |
The parameters for this method can be tweaked as necessary, they have been set for optimal generalized function:
Parameter | Function |
---|---|
DO_FASTA |
Convert BAM format to fasta format |
DO_COUNTS |
Calculate various counts statistics |
To be fixed
-
results/TAXON1_Intergenic.arg
details of arguments