Command Line Tool API

This page contains a description of all the subcommand inputs of the command line tool velocyto. For a usage guide refer to the command line tool tutorial

velocyto

velocyto [OPTIONS] COMMAND [ARGS]...

run

Runs the velocity analysis outputing a loom file

BAMFILE bam file with sorted reads

GTFFILE genome annotation file

velocyto run [OPTIONS] BAMFILE GTFFILE

Options

-b, --bcfile <bcfile>

Valid barcodes file, to filter the bam. If –bcfile is not specified all the cell barcodes will be incuded. Cell barcodes should be specified in the bcfile as the CB tag for each read

-o, --outputfolder <outputfolder>

Output folder, if it does not exist it will be created.

-e, --sampleid <sampleid>

The sample name that will be used to retrieve informations from metadatatable

-s, --metadatatable <metadatatable>

Table containing metadata of the various samples (csv formatted, rows are samples and cols are entries)

-m, --repmask <repmask>

.gtf file containing intervals to mask

-l, --logic <logic>

The logic to use for the filtering (default: Default)

-M, --multimap

Use reads that did not map uniquely (default: False)

-x, --molrep

Outputs pickle files with containing a sample of the read mappings supporting molecule counting. (Useful for development or debugging only)

-@, --samtools-threads <samtools_threads>

The number of threads to use to sort the bam by cellID file using samtools

--samtools-memory <samtools_memory>

The number of MB used for every thread by samtools to sort the bam file

Arguments

BAMFILE

Required argument

GTFFILE

Required argument

run10x

Runs the velocity analysis for a Chromium 10X Sample

10XSAMPLEFOLDER specifies the cellranger sample folder

GTFFILE genome annotation file

velocyto run10x [OPTIONS] SAMPLEFOLDER GTFFILE

Options

-s, --metadatatable <metadatatable>

Table containing metadata of the various samples (csv fortmated rows are samples and cols are entries)

-m, --repmask <repmask>

.gtf file containing intervals to mask

-l, --logic <logic>

The logic to use for the filtering (default: Default)

-M, --multimap

Use reads that did not map uniquely (default: False)

-@, --samtools-threads <samtools_threads>

The number of threads to use to sort the bam by cellID file using samtools

--samtools-memory <samtools_memory>

The number of MB used for every thread by samtools to sort the bam file

Arguments

SAMPLEFOLDER

Required argument

GTFFILE

Required argument