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lnblum
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Apr 17, 2025
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a future update could include running freebayes on only the target regions but if I recall we had some issues scaling that up and ended up running it on everything then filtering after.
lnblum
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Apr 17, 2025
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going to default to outputting to the process name, so strelka and freebayes go to separate folders
lnblum
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Apr 18, 2025
| tracedir = "${params.outdir}/pipeline_info" | ||
| run_strelka = true | ||
| run_freebayes = true | ||
| freebayes_qual_filter = 15 // default quality filter for freebayes output. |
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freebayes didn't have a standard quality filtering like strelka, so we used a basic quality filter to discard lots of false positive variants before running the concordance analysis.
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