Skip to content

Commit

Permalink
Merge remote-tracking branch 'origin/fixes' into fixes
Browse files Browse the repository at this point in the history
  • Loading branch information
gnefedev committed Oct 23, 2024
2 parents 7df90c2 + cd50c29 commit 8953bae
Showing 1 changed file with 14 additions and 4 deletions.
18 changes: 14 additions & 4 deletions regression/cli-help/findShmTrees.txt
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
Usage: mixcr findShmTrees [--v-gene-names <gene_name>]... [--j-gene-names <gene_name>]...
[--cdr3-lengths <n>]... [--min-count <n>] [--productive-only]
[--dont-combine-tree-by-cells] [-O <key=value>]... [--report <path>]
[--json-report <path>] [--use-local-temp] [--threads <n>]
[--force-overwrite] [--no-warnings] [--verbose] [--help] (input_file.
clns|directory)... output_file.shmt
[--alleles-search-could-be-skipped] [--dont-combine-tree-by-cells] [-O
<key=value>]... [--report <path>] [--json-report <path>]
[--use-local-temp] [--threads <n>] [--force-overwrite] [--no-warnings]
[--verbose] [--help] (input_file.clns|directory)... output_file.shmt
Builds SHM trees.
All inputs must be fully covered by the same feature, have the same library produced by
`findAlleles`, the same scoring of V and J genes and the same features to align.
Expand All @@ -20,6 +20,16 @@ All inputs must be fully covered by the same feature, have the same library prod
--min-count <n> Filter clones with counts great or equal to that parameter
--productive-only Build trees only on productive clones (no stop codons in all features
and no out of frame in CDR3)
--alleles-search-could-be-skipped
In specific cases preliminary search for alleles could be skipped. For
example:
- reads were aligned on gene library for the donor, that wes found
beforehand
- data is synthetic (in biological or computational way) and don't
have natural patterns of homo-hetero zygotes
- you have homogeneous specie and have a library with all presented
genes beforehand (but better to run `findAlleles` to check that
there is no diversity)
--dont-combine-tree-by-cells
In case of data with cell groups, will not combine trees by cells.
-O <key=value> Overrides default build SHM parameter values
Expand Down

0 comments on commit 8953bae

Please sign in to comment.