apply a coverage filter for pPCP1

ktmeaton · Mar 1, 2021 · 9c86378 · 9c86378
1 parent 8ad86bb
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diff --git a/auspice/plague-phylogeography_locus-coverage.json b/auspice/plague-phylogeography_locus-coverage.json
diff --git a/config/auspice_config.json b/config/auspice_config.json
@@ -82,6 +82,61 @@
       "key": "ufboot",
       "title": "Ultrafast Bootstrap",
       "type": "continuous"
+    },
+    {
+    "key": "chrom_cov",
+    "title": "Chromosome Coverage",
+    "type": "continuous"
+    },
+    {
+      "key": "pcd1_cov",
+      "title": "pCD1 Coverage",
+      "type": "continuous"
+    },
+    {
+      "key": "pmt1_cov",
+      "title": "pMT1 Coverage",
+      "type": "continuous"
+    },
+    {
+      "key": "ppcp1_cov",
+      "title": "pPCP1 Coverage",
+      "type": "continuous"
+    },
+    {
+      "key": "pla_cov",
+      "title": "pla Coverage",
+      "type": "continuous"
+    },
+    {
+    "key": "chrom_dep",
+    "title": "Chromosome Depth",
+    "type": "continuous"
+    },
+    {
+      "key": "pcd1_dep",
+      "title": "pCD1 Depth",
+      "type": "continuous"
+    },
+    {
+      "key": "pmt1_dep",
+      "title": "pMT1 Depth",
+      "type": "continuous"
+    },
+    {
+      "key": "ppcp1_dep",
+      "title": "pPCP1 Depth",
+      "type": "continuous"
+    },
+    {
+      "key": "pla_dep",
+      "title": "pla Depth",
+      "type": "continuous"
+    },
+    {
+      "key": "ppcp1_pla_dep_ratio",
+      "title": "pPCP1 pla Depth Ratio",
+      "type": "continuous"
     }
   ],
   "filters": [

diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -11,9 +11,12 @@
 1. Create gene by gene coverage.
 1. Analyze both coverage and depth of loci.
 1. Compare gene to plasmid coverage (pla, pPCP1)
+1. Apply a coverage filter for pPCP1 plasmid.
+1. Add locus coverage info to nexus tree.
 
 ## TO-DO
 
 1. Add locus coverage output to report
 1. Check if multiqc still runs without eager output dir...
 1. Add latvia samples to database!
+1. Maybe write a function to condense exporting.
diff --git a/results/auspice/nextstrain_map_1.ORI.svg b/results/auspice/nextstrain_map_1.ORI.svg
diff --git a/results/locus_coverage/all/locus_coverage.tsv b/results/locus_coverage/all/locus_coverage.tsv