1 NA18507_part.fa contains two sequences cut from the human genome
2 build36. They were exatracted with command:
4 samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550
6 Sequence names were changed manually for simplicity. ex1.fa.fai is the
7 index for the sequence file, generated by:
11 This index file also works as the reference list file used by `import'
12 and `pileup' commands of samtools. ex1.sam.gz contains MAQ alignments
15 (samtools view NA18507_maq.bam 2:2044001-2045500;
16 samtools view NA18507_maq.bam 20:68001-69500)
18 and processed with an awk command to make everything consistent as a
21 To try samtools, you may run the following commands:
23 samtools import ex1.fa.fai ex1.sam.gz ex1.bam
24 samtools index ex1.bam
25 samtools tview ex1.bam ex1.fa
26 samtools pileup -cf ex1.fa ex1.bam
27 samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz