File ex1.fa contains two sequences cut from the human genome build36. They were exatracted with command: samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550 Sequence names were changed manually for simplicity. File ex1.sam.gz contains MAQ alignments exatracted with: (samtools view NA18507_maq.bam 2:2044001-2045500; samtools view NA18507_maq.bam 20:68001-69500) and processed with `samtools fixmate' to make it self-consistent as a standalone alignment. To try samtools, you may run the following commands: samtools faidx ex1.fa # index the reference FASTA samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM samtools index ex1.bam # index BAM samtools tview ex1.bam ex1.fa # view alignment samtools pileup -cf ex1.fa ex1.bam # pileup and consensus samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz