Hi,

I have around 30 sam files in my different directories -

 ./sff*/mapping/out.sam

So in my current directory there are around 30 directories naming sff41, sff42,...,sff71,etc and then in each directory there is sub-dir called mapping in which I have out.sam files. Now I want to-

1. Convert file from SAM to BAM format

2. Sort BAM file

3. index the bam file

One option is to do it 1 by 1 which is very annoying. I also found something on this blog but it assumes all sam files with different names in one directory. I am pasting bash script from this blog-

for sample in *.sam  
 do  
   echo $sample  
   describer=$(echo ${sample} | sed 's/.sam//')  
   echo $describer  

   # Convert file from SAM to BAM format  
   samtools view -b $sample > ${describer}.uns.bam  

   # Sort BAM file  
   samtools sort ${describer}.uns.bam ${describer}   

   # index the bam file  
   samtools index ${describer}.bam  

   # Revove intermediate files  
   rm ${describer}.uns.bam  
 done

Can anyone please suggest how to modify this according to my directories or if you have any other fast method to achieve this?

Thanks in advance.