Download | Table of Options | Subset | PED to GEN Conversion | GEN to PED Conversion | Merge | Orient | Version History | Contact |
gtool |
Platform |
File |
Linux (x86_64) Static Executable |
gtool_v0.7.5_x86_64.tgz |
Linux (x86_64) Dynamic Executable |
gtool_v0.7.5_x86_64_dynamic.tgz |
Mac OS X 10.6 (Intel) |
gtool_v0.7.5_MacOSX_10.7_Intel.tgz |
tar zxvf gtool_vX.X.X_x86_64.tgz |
example.gen | A genotype file (containing data for 11 SNPs and 5 samples). |
example.sample | A sample file. |
rs_id.txt | A file containing a list of rs_ids. |
sample_id.txt | A file containing a list of sample_ids. |
exclusion.txt | A file containing a list of rs_ids. |
sample_excl.txt | A file containing a list of sample_ids. |
example.ped | An example PED file. |
example.map | An example MAP file. |
example10,11,12.gen | Example genotype files for merging. |
example10,11,12.sample | Example sample files for merging. |
Parameters | Type | Description |
-S | Subset mode | |
--g | File | Input genotype file |
--s | File | Input sample file |
--og | File | Output genotype file. Default, append .subset to genotype file name |
--os | File | Output sample file. Default, append .subset to sample file name |
--sample_id | File | Define a subset of genotypes from a list of sample_ids |
--start | Integer | Define a subset of SNPs by position (in basepairs) in the range start ≤ position ≤ end |
--end | Integer | Define a subset of SNPs by position (in basepairs) in the range start ≤ position ≤ end |
--inclusion | File | Define a subset of SNPs to include. The --inclusion file should be a single column file with a SNP ID on each line |
--exclusion | File | Define a subset of SNPs to exclude. The --exclusion file should be a single column file with a SNP ID on each line |
--missing | Double | Define a missingness threshold over which to exclude SNPs |
--threshold | Double | Define a threshold for calling genotypes for calculating missing data |
-P | PED to GEN Conversion mode | |
--ped | File | PED format genotype file |
--map | File | MAP SNP file which accompanies the --ped file |
--og | File | Output genotype file. Default, append .gen to PED file name |
--os | File | Output sample file. Default, append .sample to PED file name |
--binary_phenotype | Flag | If set, the phenotype in the output sample file is 'B' |
--family | Flag | If set, use the family id from the PED file as ID_1 in the SAMPLE file |
--snptest1 | Flag | If set, output the SAMPLE file in SNPTEST1 format |
--num_snps | Integer | Number of SNPs in PED file |
--num_samples | Integer | Number of samples in PED file |
-G | GEN to PED Conversion mode | |
--g | File | Input genotype file |
--s | File | Input sample file |
--ped | File | Output PED file. Default, append.ped to genotype file name |
--map | File | Output MAP file. Default, append .map to genotype file name |
--phenotype | String | Name of the phenotype column in the SAMPLE file to output to PED. Default -9 (Unknown) |
--sex | String | Name of the sex column in the SAMPLE file to output to PED. If unspecified will look for a column named "sex" or "gender". Default -9 (Unknown) |
--threshold | Double | Threshold for merging genotypes from GEN probability. Default 0.9 |
--num_snps | Integer | Number of SNPs in GEN file |
--num_samples | Integer | Number of samples in GEN file |
--chr | String | Chromomsome for first column of MAP file |
--snp | Flag | |
-M | Merge mode | |
--g | File | List of input genotype files |
--s | File | List of input sample files |
--og | File | Output genotype file. Default format File1_File2_...FileN.gen |
--os | File | Output sample file. Default File1_File2_...FileN.sample |
--threshold | Double | Threshold for calling genotypes from GEN probability. Default >1 (strictcomparison). |
-O | Orient mode | |
--g | File | List of input genotype files |
--strand | File | List of SNP positions and orientations (+,-) |
--og | File | Output genotype file |
--excl | Flag | If set, then SNPs with no entry in the strand file will be excluded from the output. |
--order | Flag | If set,alleles/probabilities will be output in alphabetical order A,C,G,T. If not set, alleles will be output in same order as in GEN file |
--log | File | Name of log file. Use with -S,-P,-G,-M. Default gtool.log |
gtool -S --g example/example.gen --s example/example.sample --og example/out.gen --os example/out.sample --sample_id example/sample_id.txt |
gtool -S --g example/example.gen --s example/example.sample --og example/out.gen --os example/out.sample --sample_excl example/sample_excl.txt |
gtool -S --g example/example.gen --s example/example.sample --og example/out.gen --os example/out.sample --inclusion example/rs_id.txt |
gtool -S --g example/example.gen --s example/example.sample --og example/out.gen --os example/out.sample --exclusion example/exclusion.txt |
gtool -S --g example/example.gen --s example/example.sample --og example/out.gen --os example/out.sample --start 10015000 --end 10075000 |
gtool -S --g example/example.gen --s example/example.sample --missing 0.05 --threshold 0.9 |
chromosome | SNP_id | genetic_distance | position |
chromosome | SNP_id | genetic_distance | position | allele1 | allele2 |
22 | rs1234 | 0.001 | 1000000 | A | G |
gtool -P --ped example/example.ped --map example/example.map --og example/out.gen --os example/out.sample |
gtool -P --ped example/example.ped --map example/example.map --binary_phenotype 1 |
gtool -P --ped example/example.ped --map example/example.map --family |
gtool -G --g example/example.gen --s example/example.sample --ped example/out.ped --map example/out.map --phenotype phenotype_1 --threshold 0.9 |
gtool -G --g example/example_chr.gen --s example/example.sample --ped example/out.ped --map example/out.map --phenotype phenotype_1 --threshold 0.9 |
gtool -G --g example/example.gen --s example/example.sample |
gtool -M --g example/example10.gen example/example11.gen --s example/example10.sample example/example11.sample --log example/example10_example11.log |
./gtool -M --g example/example11.gen example/example12.gen --s example/example11.sample example/example12.sample --threshold 0.9 --log example/example11_example12.log |
position | orientation |
gtool -O --g example/example.gen --strand example/example.strand --og example/example_orient.gen --log example/example_orient.log |