This repository contains a collection of scripts that make heavy 'omics' work a bit lighter.
All scripts are annotated for debugging purposes - and future reference. The scripts will work within the context of a certain Linux environment (in this case a CentOS7 system on a SUN Grid Engine background). As such we have tested fastQTLToolKit on CentOS7, OS X El Capitan (version 10.11.[x]), and macOS Sierra (version 10.12.[x]).
checkPerlModules.pl
BETA-version. Purpose: to check the availability of certain Perl modules on the system. Will install those that are not present, and update those that are.
IMPUTE2DOSAGE
Two scripts (convert_impute2dosage.pl and convert_impute2dosage.sh) are present that can convert IMPUTE2 derived *.gen-files to PLINK-style .dosage-files.
IMPUTE2 derived imputed genotype data (*.gen-files) are genotype probabilities per genotype for each variant (AA, AB, BB). These scripts will convert these genotype probabilities to PLINK-style dosage data. The three genotype probabilities (AA, AB, BB) are converted to 1 dosage relative to the B-allele, i.e. the coded or effect allele. The resulting files can than readily be used used for polygenic scores analyses or regular PLINK-style association analyses with the --dosage flag. Output will automatically be gzipped.
Files made are:
- *.dose.gz -- the new DOSAGE file in PLINK style
- *.map -- the new MAP file in PLINK style
- *.fam -- the new FAM file in PLINK style
FURTHER NOTES:
- A [*.gen.gz] extension, i.e. a gzipped [*.gen] file is expected.
- The FAM-file only contains the sample IDs and has PID, MID, Sex and Phenotype set to -9.
Merging to (large) tables
Originally made by Paul I.W. de Bakker.
Use the mergeTables.pl to merge two (large) tables based on an index-column. Command:
merge_tables.pl --file1 datafile_1 --file2 datafile_2 --index index_string --format [GZIP1/GZIP2/GZIPB/NORM] [--replace]
Prints all contents of datafile_2, each row is followed by the corresponding columns from datafile_1 (indexed on index_string). The argument --format indicates which of the files are gzipped. If --replace is specified, only the contents of datafile_2 are output with relevant elements replaced by those in datafile_1.
metaanalyzer.R
Meta-analysis of n tables. Will be z-score, fixed-effects, and random-effects meta-analysis of each row indexed by a key-variable (e.g. SNP, CpG, Gene). Requires: key-variable, beta (effect size), s.e. (standard error), p-value, n (sample size).
numberoffields.pl
Calculates the number of fields per row in a file.
overlap.pl
Find the overlap between two files.
overlap.pl datafile_1 [column-number] datafile_2 [column-number] > new_datafile_3
removedupes.pl
Remove duplicate rows in a file. Three arguments are required: original-filename, gzip/norm, and new-filename.
removedupes.pl datafile_1 [GZIP/NORM] new_datafile_1
[GZIP/NORM]: indicates whether the original file (datafile_1) is gzipped (GZIP) or not (NORM).
uniquefy.pl
Make a given list (in a file) unique.
uniquefy.pl datafile_1 > new_datafile_1
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