Utility actions

Version info

In order to check the current version of MiXCR as usual one can use -v option:

> mixcr -v
MiXCR v2.1 (built Mon Feb 06 19:56:13 MSK 2017; rev=a9958cd; branch=release/v2.1)
RepSeq.IO v1.2.6 (rev=958e019)
MiLib v1.7.1 (rev=f6ccdbc)
Built-in V/D/J/C library: repseqio.v1.2

Library search path:
- built-in libraries
- /Users/dbolotin/.
- /Users/dbolotin/.mixcr/libraries

In order to check which version of MiXCR was used to build some vdjca/clns file:

> mixcr versionInfo file.vdjca
MagicBytes = MiXCR.VDJC.V06
MiXCR v1.8-SNAPSHOT (built Fri Jan 29 16:16:40 MSK 2016; rev=327c30c; branch=feature/mixcr_diff); MiLib v1.2 (rev=4f56782; branch=release/v1.2); MiTools v1.2 (rev=eb91603; branch=release/v1.2)

Merge alignments

Allows to merge multiple .vdjca files into a single one:

> mixcr mergeAlignments file1.vdjca file2.vdjca ... output.vdjca

Filter alignments

Allows to filter alignments in .vdjca file. Example:

> mixcr filterAlignments --chains TRA,TRB input_file.vdjca output_file.vdjca

The available options are:

Option Description
-e, --cdr3-equals Include only those alignments which CDR3 equals to a specified nucleotide sequence
c, --chains Include only alignments with specified immunological protein chains (comma separated list of some of IGH, IGL, IGK, TRA, TRB, TRG, TRD chains)
-x, --chimeras-only Output only chimeric alignments
-g, --contains-feature Include only those alignments that contain specified gene feature (see Gene features and anchor points)
-i, --read-ids Output alignments with specified IDs only
-n, --limit Maximal number of alignments to process