A collection of SLURM batch submission and accessory scripts for BigPurple - NYU Langone Health HPC
Each script includes a help message that can be displayed the same for all: ./script.sh -h
| Script | Quick Description |
|---|---|
bamMerger.sh |
merge all BAMs within a directory |
cramConverter.sh |
convert all CRAMs within a directory into BAMs |
egaDataDownloader.sh |
download EGA data into a subdirectory |
fileRenamer.sh |
rename files within a directory based on file of names |
neatGenReads.sh |
simulate genomic reads to produce PE FASTQs and gold standard BAM/VCF |
sftpBackgroundExecutor.sh |
executes a series of SFTP commands in the background |
sraFastqExtractor.sh |
dump the FASTQs from SRA data into a subdirectory |
sraFilePrefetcher.sh |
prefetch SRA data into a subdirectory |
tidyBam.sh |
tidy up BAM by removing any unmapped reads with non-zero MAPQ |
vcfSampleExtractor.sh |
extract all records in a VCF for a given sample |
| Script | Quick Description |
|---|---|
hintPre.sh |
perform the preprocessing step of HiNT pipeline |
sambambaFlagstat.sh |
quality check of alignment metrics after preprocessing |
hintCnv.sh |
perform the CNV calling step of HiNT pipeline |
hintTl.sh |
perform the translocation calling step of HiNT pipeline |
hintWorkflow.sh |
wrapper script to run HiNT pipeline using SLURM |