Basic Samtools

Count number of records per reference in bamfile

samtools idxstats thing.bam

Convert sam into bam (and back again)

Samtools can be used to convert between sam and bam:

• -b indicates that the input file will be in BAM format
• -S indicates that the stdout should be in SAM format

samtools view -sB thing.bam > thing.sam

And to convert between sam and bam:

samtools view thing.sam > thing.bam
samtools sort thing.bam thing
samtools index thing.bam

This will produce a sorted, indexed bam. This will create the files thing.bam and thing.bam.bai. To use a bam you must have an index file.