broadinstitute / viral-phylo

viral-ngs: phylogenetics, annotation, intrahost variants
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add alternative to V-Phaser2 for iSNV calling #28

Open tomkinsc opened 4 years ago

tomkinsc commented 4 years ago

We should have an alternative option or replacement for V-Phaser2 for iSNV calling. V-Phaser2 is not actively maintained and does not tolerate single-end reads.

We should be able to change the code to parse the output of another tool or pileup-based process.