Commits for angie

4baf9e8d58909435aeff4102172d4b6c76e9ed0c Sun Apr 19 11:43:07 2020 -0700

Better Nextstrain VCF (merge SNVs at same pos, add BACKMUTS); new output file .varPaths. refs #25188 VCF improvements: * Merge SNVs at the same position (multiple alt alleles like C>A and C>T, serial mutations like T>G and G>A, and back-mutations like G>T and T>G) into a single VCF record with accurate allele counts. * Add BACKMUTS to INFO to highlight samples with back-mutations. The new output file nextstrainSamples.varPaths shows the sequence of variants that occur at nodes in the path from the root of the tree to the sample's leaf, for each sample. This gives some insight into the strucure of the tree and how many mutations the various samples have; by comparing .varPaths files from different NextStrain releases, we can also see that the order of ancestors and descendants is sometimes shuffled from one release to the next.
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 122, context: html, text, full: html, text

8548ce2dc690933cbc0ba86b02260401fdc1682e Sun Apr 19 12:00:01 2020 -0700

Add timestamp to ncov.json filename since there can be interesting changes within a single day and we need to have reproducible analyses. refs #25188
- src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 4, context: html, text, full: html, text

03c00c97bfb4666cbc74b63bf06a62948ff643ee Sun Apr 19 14:36:54 2020 -0700

Add -f now that I'm write-protecting the timestamped ncov.json copies. refs #25188
- src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 1, context: html, text, full: html, text

b22c1c39b539a7e6167cf41983d09ce6cbf243e8 Mon Apr 20 21:16:43 2020 -0700

Add submitting_lab to .varPaths file. Compute tree parsimony score for each recurrent biallelic variant for David. refs #25188
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 131, context: html, text, full: html, text

fc3a8ce57297d0b2bbff8f7acbb3cc90dfe601eb Mon Apr 20 23:41:28 2020 -0700

Changing udc.localDir from /gbdb/hubs (which doesn't exist) to just /gbdb so I can install some files in /gbdb but make them custom tracks for now. refs #25188
- confs/hgwdev.hg.conf - lines changed 1, context: html, text, full: html, text

17ef8d906cb3af6d9426b80b1962e1948f5e9ade Mon Apr 20 23:51:42 2020 -0700

Automatically update the experimental custom tracks for David so that they stay in sync with the updated VCF. refs #25188
- src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 30, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/makefile - lines changed 1, context: html, text, full: html, text

2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700