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igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
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Down-sampling #61

Closed azbard closed 2 years ago

azbard commented 2 years ago

Is downsampling supported? The files I'm producing are way too large.

jrobinso commented 2 years ago

No, there is no downsampling option prior to creating the report. This is complex, if we downsample before producing the report igv.js will not see all the reads and the coverage will be misleading. If that is acceptable we could probably add a downsampling option with pysam. I don't know when I could get to that, to be honest, in the meantime I suggest you downsample your bam file with samtools before running igv-reports.