Are [*.removed.sorted.bai] and [*.metrix.txt] needed for the next step?

Question

[Hyeong Seok]

I am new to bioinformatics and now I am on WES...

My server has limited capacity, so I removed files for the previous step.

On the way of sequencing, I got wrong [*.removed.sorted.bam] files without removing duplicates.

By using samtools view -F 1024, I got right [*.removed.sorted.bam] files.

However, I have no idea how to get right [.removed.sorted.bai] and [.metrix.txt] files from [*.removed.sorted.bam] files.

Are these files needed for the further steps? Or do I only need [*.removed.sorted.bam] files?

Thank you for your help!

Answer 1

[Devon Ryan]

Any .bai file is made with samtools index. I expect the .metric.txt is made with samtools idxstats or some custom script, or perhaps some tool from picard to collect on-target metrics (have a look there). having on-target metrics is useful just to keep an eye on things.