Reset the Subject Names
Use the following command to reset subject (or sample) names of GTB:
reset-subject <input> -o <output> [options]
Program Options
Usage: reset-subject <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.
--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
'--subject @file'.
format: --subject <string>,<string>,...
--prefix Use the format `[prefix][number][suffix]` to reset the subject
names.
default: S_
format: --prefix <string>
--suffix Use the format `[prefix][number][suffix]` to reset the subject
names.
format: --suffix <string>
--begin Use the format `[prefix][number][suffix]` to reset the subject
names.
default: 1
format: --begin <int>
Example
Use the GBC to compress an example file ./example/rare.disease.hg19.vcf.gz
:
# Linux or MacOS
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc \
build ./example/rare.disease.hg19.vcf.gz -o ./example/rare.disease.hg19.gtb -y
# Windows
docker run -v %cd%:./gbc/ -w ./gbc/ --rm -it -m 4g gbc build ./example/rare.disease.hg19.vcf.gz -o ./example/rare.disease.hg19.gtb -y
Reset the subject names to CASE_6_1
, CASE_7_1
and CASE_8_1
:
# Linux or MacOS
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc \
reset-subject ./example/rare.disease.hg19.gtb -o ./example/out.gtb --prefix CASE_ --begin 6 --suffix _1 -y
# Windows
docker run -v %cd%:./gbc/ -w ./gbc/ --rm -it -m 4g gbc reset-subject ./example/rare.disease.hg19.gtb -o ./example/out.gtb --prefix CASE_ --begin 6 --suffix _1 -y
or:
# Linux or MacOS
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc \
reset-subject ./example/rare.disease.hg19.gtb -o ./example/out.gtb --subject CASE_6_1,CASE_7_1,CASE_8_1 -y
# Windows
docker run -v %cd%:./gbc/ -w ./gbc/ --rm -it -m 4g gbc reset-subject ./example/rare.disease.hg19.gtb -o ./example/out.gtb --subject CASE_6_1,CASE_7_1,CASE_8_1 -y