SAM/BAM Sequence Alignment

An alignment file provides context for raw data. It has 11 tab-delimited columns with one alignment record per line.

SAM is plain-text (human readable), whereas BAM is in binary format.

SAMTools is a suite of utilities for SAM/BAM files. Picard is a set of tools for sequencing data.

Example SAM file

D4ZHLFP1:53:D2386ACXX:6:2115:17945:68812 0 Mle_000001 18 42 108M * 0 0
    TCCCCCTGCATGGTCCGTCTGCGTGCAATCGCATGAGTATGCCTCCAGCATGAGTTACCGATCGTGGACACCTGCTTG
GCCAAGATGTACTGAGATGCAT
C@CFDEFFHHGHHFGBGFEGGDGGGEHGHGGGJJJJIIGIIB9BFBFHGHHICEAHGGEGEDHIGEEDBECCACBDDC@CCDBCDD<
?2+4>@4>>CCCAA@@  AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0A107 
    YT:Z:UU
D4ZHLFP1:53:D2386ACXX:7:2110:5214:83081 0 Mle_000001 18 42 108M * 0 0
TCCCCCTGCATGGTCCGTCTGCGTGCAATCGCATGAGTATGCCTCCAGCATGAGTTACCGATCGTGGCAACCTGCTTGCCAA
GATGTACTGAGATGCAT
CCCFFFFHHHHHHHGGGEGIJIIGJFHJJJJIJIJJIJIJGIJJIJJIJFHJJJIJJHHFFCEEEEEDDDDDDDDDDDDD  AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0A107      
    YT:Z:UU
D4ZHLFP1:53:D2386ACXX:7:2206:9985:31556 0 Mle_000001 18 42 108M * 0 0
TCCCCCTGCATGGTCCGTCTGCGTGCAATCGCATGAGTATGCCTCCAGCATGAGTTACCGATCGTGGCAACCTGCTTGCCAA
GATGTACTGAGATGCAT
CCCEFFFFHHHHHJJIJHJJIJIJJIJIJJJJIJIJJJIJJIJJJIJJJGEFFEEEEDDDDDDDDDDDDDDDDDDDDDDD  AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0A107 
    YT:Z:UU

Helpful site for looking up SAM flags: https://broadinstitute.github.io/picard/explain-flags.html