Sam 文件格式详解

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An alignment of a read to a single reference sequence that may include insertions,deletions, skips and clipping, but may not include direction changes (i.e., one portion of the alignment on forward strand and another portion of alignment on reverse strand). A linear alignment can be represented in a single SAM record.

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An alignment of a read that cannot be represented as a linear alignment. A chimeric alignment is represented as a set of linear alignments that do not have large overlaps. Typically, one of the linear alignments in a chimeric alignment is considered the “representative” alignment, and the others are called “supplementary” and are distinguished by the supplementary alignment flag. All the SAM records in a chimeric alignment have the same QNAME and the same values for 0x40 and 0x80 flags (see Section 1.4). The decision regarding which linear alignment is representative is arbitrary（任意的）.

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A linear alignment or a chimeric alignment that is the complete representation of the alignment of the read.

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The correct placement of a read may be ambiguous, e.g., due to repeats. In this case, there may be multiple read alignments for the same read. One of these alignments is considered primary. All the other alignments have the secondary alignment flag set in the SAM records that represent them. All the SAM records have the same QNAME and the same values for 0x40 and 0x80 flags. Typically the alignment designated primary is the best alignment, but the decision may be arbitrary.

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samtools view -H mapped.sam 
#bam文件也可以

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samtools view -H mapped.sam |grep "^@SQ"

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samtools view -H mapped.sam |grep "^@PG"

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Samtools view mapped.sam |head -n 1

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samtools view mapped.sam |tr '\t' '\n'|head -n 11
#tr '\t' '\n'：将\t——tab换成\n回车符，即换行

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samtools flags
##
Flags:
	0x1	PAIRED        .. paired-end (or multiple-segment) sequencing technology
	0x2	PROPER_PAIR   .. each segment properly aligned according to the aligner
	0x4	UNMAP         .. segment unmapped
	0x8	MUNMAP        .. next segment in the template unmapped
	0x10	REVERSE       .. SEQ is reverse complemented
	0x20	MREVERSE      .. SEQ of the next segment in the template is reversed
	0x40	READ1         .. the first segment in the template
	0x80	READ2         .. the last segment in the template
	0x100	SECONDARY     .. secondary alignment
	0x200	QCFAIL        .. not passing quality controls
	0x400	DUP           .. PCR or optical duplicate
	0x800	SUPPLEMENTARY .. supplementary alignment
	##

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samtools flags 147
##
0x93	147	PAIRED,PROPER_PAIR,REVERSE,READ2
##

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samtools flags Paired，read2
##
0x41	65	PAIRED,READ1
##

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samtools view -b mapped.sam > mapped.bam

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samtools view mapped.bam > mapped.sam
#没有header的sam文件不能转bam文件，ru
Samtools view -b mapped.sam > mapped.bam
#报错：

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samtools view -h mapped.bam > mapped.sam

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samtools sort mapped.bam > mapped.sorted.bam

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samtools sort -@ 4 -m 8G mapped.bam > mapped.sorted.bam

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samtools index mapped.sorted.bam
#生成mapped.sorted.bam.bai

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samtools view mapped.sorted.bam reftig_23:715574-715600 |head -n 3
##
...
ST-E00299:129:HMTFKCCXX:2:1113:28777:2856	147	reftig_23	715428	60 [...]
...
##

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samtools view mapped.sorted.bam reftig_23:715574-715600 > new.sorted.bam

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samtools flags unmap
0x4	4	UNMAP

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samtools view -f 4 mapped.bam 

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samtools view -f 4 mapped.bam ｜head -n 3

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samtools flags 113
0x85	133	PAIRED,UNMAP,READ2
samtools flags 77
0x4d	77	PAIRED,UNMAP,MUNMAP,READ1

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samtools flags read1，proper_pair
0x42	66	PROPER_PAIR,READ1
samtools view -f 66 mapped.sam > mapped.youwant.bam

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samtools view -F 4 mapped.bam > mapped.hits.bam