Usefull small commands scripts etc

Quick command to index a bunch of bam files

Use case:

• you have a set of bam files, some (or all) of which are not yet indexed
• you want to run 'samtools index' on those that are not yet indexed
• (optional) you would like to run this in parallel

Solution: use the makefile I created for this: /projects/cees/scripts/makefiles/index_all_bams.mk

Usage:

cd path/to/folder/with/bam/files
module load samtools
make -f /projects/cees/scripts/makefiles/index_all_bams.mk

To run this in parallel, add the '-j' flag and the number of threads to start:

make -j 5 -f /projects/cees/scripts/makefiles/index_all_bams.mk

Output:

• For each .bam file, a corresponding .bam.bai file

Notes:

• if any .bam file present in the folder already has a corresponding .bam.bai file, his bam file will not be indexed

Author: Lex Nederbragt