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After doing some initial data preparation steps, PBS consists of doing:
an allele count for each population.
sgkit.count_alleles will do this.
locate and subset to segregating variants at sufficient frequency.
-requires an is_biallelic_01 function.
-requires a to_frequencies function, or some equivalent operation.
setup windows over the genome.
-requires a moving_statistic function.
calculate the PBS in a moving window.
-requires a pbs function.
After doing some initial data preparation steps, PBS consists of doing:
sgkit.count_alleles
will do this.-requires an
is_biallelic_01
function.-requires a
to_frequencies
function, or some equivalent operation.-requires a
moving_statistic
function.-requires a
pbs
function.Here is the notebook that @alimanfoo made.
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