Setup GBC
Launch the GBC in the command line program (terminal) with the following command:
# The program document is printed by default when no parameters are passed in.
java -Xms4g -Xmx4g -jar gbc.jar
# When passing -h, -help or --help, the program will also print the program document.
java -Xms4g -Xmx4g -jar gbc.jar -h
The results are as follows:
Usage: java -jar gbc.jar [mode/tool] [options]
Version: GBC-1.2 (last edited on 2022.06.20, http://pmglab.top/gbc)
Mode:
build Compress and build *.gtb for vcf/vcf.gz files.
format: build <input(s)> -o <output> [options]
extract Retrieve variants from *.gtb file, and export them to
(compressed) VCF format or GTB format.
format: extract <input> -o <output> [options]
show Display summary of the GTB File.
format: show <input> [options]
sort Sort variants in GTB by coordinates (chromosome and position).
format: sort <input> -o <output> [options]
concat Concatenate multiple VCF files. All source files must have the
same subjects columns appearing in the same order with
entirely different sites, and all files must have to be the
same in parameters of the status.
format: concat <input(s)> -o <output> [options]
merge Merge multiple GTB files (with non-overlapping subject sets)
into a single GTB file.
format: merge <input(s)> -o <output> [options]
reset-subject Reset subject names (request that same subject number and no
duplicated names) for gtb file directly. Subject names can be
stored in a file with ',' delimited form, and pass in via
'--reset-subject @file'.
format: reset-subject <input> -o <output> [options]
prune Prune GTB files by node-level or chromosome-level.
format: prune <input> -o <output> [options]
allele-check Correct for potential complementary strand errors based on
allele labels (A and C, T and G; only biallelic variants are
supported).
format: allele-check <template_input> <input> -o <output>
[options]
split Split a single GTB file into multiple subfiles (e.g. split by
chromosome).
format: split <input> -o <output> [options]
ld Calculate pairwise the linkage disequilibrium or genotypic
correlation.
format: ld <input> -o <output> [options]
index Index contig file for specified VCF file or reset contig file
for specified GTB file.
format: index <input (VCF or GTB)> -o <output> [options]
Tool:
bgzip Use parallel bgzip to compress a single file.
format: bgzip <string> <string> ...
md5 Calculate a message-digest fingerprint (checksum) for file.
format: md5 <string> <string> ...
download Download resources from an URL address.
format: download <string> <string> ...
update Update GBC software packages.
default: ./gbc.jar
format: update <gbc.jar>
Use GBC in interactive mode
When running program commands multiple times with GBC, we recommend doing so in interactive mode (like ipython), which provides real-time feedback on program input and reduces the time required to start the JVM (especially when running in Docker, using interactive mode avoids frequent container creation and destruction). To start interactive mode, run:
java -Xmx4g -Xms4g -jar gbc.jar -i
Of course, the user can also choose to enter interactive mode after running the command once, with the following command:
java -Xmx4g -Xms4g -jar gbc.jar [mode/tool] [options] -i
When you type a command, you no longer need to specify java -Xmx4g -Xms4g -jar gbc.jar
. The command line interaction mode has four additional parameters in addition to the parameters in command line mode:
Parameters | Description |
---|---|
exit, q, quit | Exit program, exit the command line interaction mode. |
clear | Clearing the screen (actually printing out multiple blank lines). |
Lines begin with "#" | For annotation. |