Read In Function for BAM file processing

Question

[Jonas.Koch]

Hi all,

I want to write a bash script that reads in a BAM file and performs several processing steps with that input file.

Can you recommend some ideas to write such a script? I am a beginner and would be very happy for some input. We want to extract mapped and unmapped reads of the BAM files. I have already written the commands for these purposes, but I don't know how to write such a read in function. Otherwise, I would have to type in all commands again and again for each BAM file.

Many greetings!

[i.sudbery]

can you show us an outline of what this might look like for a single file?

[GenoMax]

Providing you with a skeleton to play with. Remove word echo once your command lines look sane to actually run.

for file in *.bam
do name=$(basename $file .bam) 
# re-use ${name} as needed to reconstruct new file names with relevant steps
echo samtools sort -o ${name}_sorted.bam ${name}.bam
echo samtools view -F 256 ${name}.bam ....
done