Prune GTB Tree
Use the following command to prune the GTB Tree:
prune <input> -o <output> [options]
Compared with extract
, prune
does not need to decompress any data for node extraction or deletion, which is faster and less memory-intensive, and all operations can be completed in seconds.
Program Options
Usage: prune <input> -o <output> [options]
Options:
--contig Specify the corresponding contig file.
default: /contig/human/hg38.p13
format: --contig <file> (Exists,File,Inner)
*--output,-o Set the output file.
format: --output <file>
--yes,-y Overwrite output file without asking.
--delete-node Delete the specified GTBNodes.
format: --delete-node <string>:<int>,<int>,... <string>:<int>,<int>,... ...
--retain-node Retain the specified GTBNodes.
format: --retain-node <string>:<int>,<int>,... <string>:<int>,<int>,... ...
--delete-chrom Delete the specified Chromosomes.
format: --delete-chrom <string>,<string>,...
--retain-chrom Retain the specified Chromosomes.
format: --retain-chrom <string>,<string>,...
Example
Use the GBC to extract the sex chromosomes (chrX and chrY) of 1000GP3.gtb
.
# Linux or MacOS
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc \
prune ./example/1000GP3.gtb -o ./example/1000GP3.chrXY.gtb \
--retain-chrom X,Y \
-y
# Windows
docker run -v %cd%:./gbc/ -w ./gbc/ --rm -it -m 4g gbc prune ./example/1000GP3.gtb -o ./example/1000GP3.chrXY.gtb --retain-chrom X,Y -y
View the summary information of extracted GTB file:
# Linux or MacOS
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc \
show ./example/1000GP3.chrXY.gtb --add-tree
# Windows
docker run -v %cd%:./gbc/ -w ./gbc/ --rm -it -m 4g gbc show ./example/1000GP3.chrXY.gtb --add-tree
Here, the terminal prints the following message:
Summary of GTB File:
GTB File Name: /Users/suranyi/Documents/project/GBC/GBC-1.1/example/1000GP3.chrXY.gtb
GTB File Size: 66.759 MB
Genome Reference: ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
Suggest To BGZF: false
Phased: true
Ordered GTB: true
BlockSize: 16384 (-bs 7)
Compression Level: 16 (ZSTD)
Dimension of Genotypes: 2 chromosomes, 3530137 variants and 2504 subjects
Summary of GTB Nodes:
├─ Chromosome X: posRange=[60020, 155260478], numOfNodes=212, numOfVariants=3468095
└─ Chromosome Y: posRange=[2655180, 28770931], numOfNodes=4, numOfVariants=62042