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
Copyright ©Liubin Zhang all right reservedLast modified time: 2022-07-12 07:48:30

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