Pre-Processing Bam Files 🐢

Before doing a large SNP calling exercise, I needed to sort and index all the BAM files that we’ll be working with.


February 20, 2023

For this, I wanted to sort, mark duplicates, and index each of the bam files we are working with. I softlinked all the bam files into a new folder called processing via for file in ../samples/all005/*.bam; do ln -s $file; done.

Then I fired up R and loaded the latest modeule on the server module load R/4.1.2 and then hooked up VSCode over SSH to write the following snippet.

library( tidyverse )

bam <- list.files("./processing", pattern=".bam", full.names=TRUE)
for( i in 1:length(bam) ) { 
    file <- bam[i]
    base <- str_replace( file, pattern="-RG.bam", replacement="")

    fsorted <- paste( base, "-sorted.bam", sep="")
    cmd <- paste( "samtools sort", file, "-o", fsorted )
    system( cmd )

    mdfile <- paste( base, "-sorted-md.bam", sep="")
    cmd <- paste( "samtools markdup", fsorted, mdfile )
    system( cmd )

    cmd <- paste( "samtools index", mdfile)
    system( cmd )

    cat( i, base, "\n")

Running this made several derivded files for each one, a sorted one, a one with marked duplicates, and one that had the index on it. So now each sample looks like this.

[rjdyer@huff10 4_processing]$ ls -1 Zoo_969*
Zoo_969-RG.bam -> ../samples/all005/Zoo_969-RG.bam

After testing to make sure the commands were properly set up, I ran the script in as a batch. It didn’t take that long to finish, maybe 3-4 seconds per sample.