NOTE: These files were copied from the examples directory in the
Samtools distribution version 0.1.3. The original README follows.

ORIGINAL 00README.txt

File ex1.fa contains two sequences cut from the human genome
build36. They were extracted 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

