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Usage

bip [command] **params

Command	Alias	Description
bam_counts		Get counts from BAM file.
compile_bam_stats	cbs	Complies BAM stats to CSV.
bedfilegenerator	bfg	Generate and sort BED files from a parsed GTF file.
panelgenequery	pgq	Using an intersected bedfile, produces a file with gene presence information.
downsample		Pipeline to map, deduplicate, and downsample sequencing reads.
fastq_read_counter	frc	Count reads from FASTQ file.
fastqvalidate	fqv	Validate fastq files in a given directory using fastQValidator.
merge_it	mff	Merge FASTQ files.
undetermined_demultiplexer	ud	Filter undetermined FASTQ files for multiple samples using index information.
remove_undetermined_fastq	ruf	Remove undetermined FASTQ files (recursively) from a directory.
is_mounted		Check if a given path is a mounted server.
mount_server		Mount a server.
check_reconnect		Check reconnects.
md5sumchecker	md5sc	Check md5sum of a file.
check_gzip_validity	cgv	Check a compressed file validity.
nipt_bcl2fastq	nb2f	Run bcl2fastq conversion for multiple BCL folders.

Options

Option	Description
-h, --help	Show this help message and exit
--version, -v	Show version