utils

Repo filled with little useful bioinformatics scripts

alter_vcf.sh - alters vcf to add or remove chr naming convention used by CellRanger so that BAM file and VCF match (much quicker to edit VCF file)

pipeline.sh - manipulates SAM, BAM and CRAM files so that the chr naming convention used by CellRanger is added or removed, reorders the header as chr naming convention orders head chr1, chr10, chr11 etc, resorts BAM file to match new header and removes contigs. Also generates files listing chromosomes and contigs present in BAM and VCF file to check naming convention matches.

remove_contigs.sh - removes extra contigs added to BAM files by processes such as Starsolo

move-fastqs.sh - combines fastq label with cram label and moves to a new directory so that starsolo can execute on uniquely labelled fastqs

add_assignee.sh - adds a new file to each ticket in our teams ticket structure with the information on who the jira ticket is assigned to

wget_parallel.sh - parallelises downloading files using wget and xargs

bz2_to_gz.sh - parallelises the conversion of bz2 to gz

generic-bsub.sh - illustrates the concept of how to bsub properly

bsub_bam_to_fastq.sh - script that converts bams to fastqs on Sanger FARM

generic-job-array-bsub.sh - illustrates dynamic bsub job array submission utilising inputted sample file

fix-erroneous-reads.sh - illustrates how to fix fastq files that have inconsistent read lengths

parallel_aws_copy.sh - illustrates parallelising S3 copy commands into chunks