#samtools

A postdoc in my lab today was asking me how to compress SAM files back to BAM files. This was apparently nonintuitive to him so I decided to write a quick post on minor details regarding this type of conversion with samtools, a great set of utilities for handling high throughput sequence alignment files:

Before you perform the actual conversion, you’ll want to first check if your SAM file contains a header:

head yourFile.sam

If a header exists, you should see lines beginning with “@”. If this is the case, you’ll want to use the -b flag to signify the output should be BAM and the -S flag to signify the input is in SAM format. Because the header is present you don’t need to include a reference fasta file for samtools to index through–meaning you can proceed as follows:

SAM –> BAM if header is present

samtools view  -bS yourFile.sam > youFile.bam

If “@” is missing from the head you did above, you’ll want use the -bT flags. 

SAM –> BAM if header is missing

samtools view -bT reference.fa yourFile.sam > yourFile.bam

You’ll probably want to sort your BAM file, considering sorted BAMs are often the useful files for myriad programs. 

samtools sort yourFile.bam yourFile_sorted

And lastly, you’ll want to index your BAM file as this is also useful for further analyses on your alignments

samtools index yourFile_sorted.bam yourFile_sorted.bai

bowtie reference -SC -q .fastq | samtools view -Shu - | samtools sort - name.sorted.prefix samtools index name.sorted.prefix.bam samtools idxstats name.sorted.prefix.bam > stats.txt