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tool for variant info across genomic windows #14

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arq5x opened this issue Apr 19, 2012 · 1 comment
Closed

tool for variant info across genomic windows #14

arq5x opened this issue Apr 19, 2012 · 1 comment

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@arq5x
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arq5x commented Apr 19, 2012

Write a generic tool for reporting BEDGRAPH variation stats for windows across the genome.

For example, using the nucl_diversity column in the variants table, we can report a BEDGRAPH of the average nucleotide diversity in each window:

chr1 10000 20000 2.3
chr1 20000 30000 3.7
...

Use pybedtools.window_maker to generate the windows, along with mapbed to do the calculations. Should be easy and quite powerful.
@arq5x
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arq5x commented May 24, 2012

Addressed with 499e5516f9

@arq5x arq5x closed this as completed May 24, 2012
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