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1 File ex1.fa contains two sequences cut from the human genome
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2 build36. They were exatracted with command:
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3
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4 samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550
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5
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6 Sequence names were changed manually for simplicity. File ex1.sam.gz
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7 contains MAQ alignments exatracted with:
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8
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9 (samtools view NA18507_maq.bam 2:2044001-2045500;
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10 samtools view NA18507_maq.bam 20:68001-69500)
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11
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12 and processed with `samtools fixmate' to make it self-consistent as a
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13 standalone alignment.
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14
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15 To try samtools, you may run the following commands:
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16
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17 samtools faidx ex1.fa # index the reference FASTA
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18 samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM
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19 samtools index ex1.bam # index BAM
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20 samtools tview ex1.bam ex1.fa # view alignment
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21 samtools pileup -cf ex1.fa ex1.bam # pileup and consensus
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22 samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz
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23
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