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| \documentclass[10pt]{article} | ||
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| \addtolength{\textwidth}{3.2cm} | ||
| \addtolength{\hoffset}{-1.6cm} | ||
| \addtolength{\textheight}{4cm} | ||
| \addtolength{\voffset}{-2cm} | ||
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| \makeindex | ||
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| \title{The SAM Format Specification (v1.3 draft)} | ||
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| \begin{document} | ||
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| \maketitle | ||
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| \section{Terminologies and Concepts} | ||
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| \begin{description} | ||
| \item[Template] A DNA/RNA sequence part of which is sequenced on a | ||
| sequencing machine. | ||
| \item[Fragment] A (sub)sequence on a template which is | ||
| sequenced. Fragments on a template are said to be \emph{ordered} if | ||
| the their relative positions on the template are known. In this case, | ||
| the template is also said to be ordered. | ||
| \item[Read] A raw sequence that comes off a sequencing machine. A read | ||
| may consist of multiple fragments. | ||
| \item[1-based coordinate system] A coordinate system where the first | ||
| base of a sequence is one. In this coordinate system, a region is | ||
| specified by a closed interval. For example, the region between the 3rd | ||
| and the 7th bases inclusive is $[3,7]$. The SAM and GFF formats are | ||
| using the 1-based coordinate system. | ||
| \item[0-based coordinate system] A coordinate system where the first | ||
| base of a sequence is zero. In this coordinate system, a region is | ||
| specified by a half-close-half-open interval. For example, the region | ||
| between the 3rd and the 7th bases inclusive is $[2,7)$. The BED, | ||
| Wiggle and PSL formats are using the 0-based coordinate system. | ||
| \end{description} | ||
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| \section{The SAM Format Specification} | ||
| \subsection{The header} | ||
| The header section can be absent. | ||
| \begin{center} | ||
| \begin{tabular}{|l|l|p{13.5cm}|} | ||
| \hline | ||
| \multicolumn{2}{|l|}{\bf Tag} & {\bf Description} \\ | ||
| \hline | ||
| \multicolumn{2}{|l}{\tt @HD} & The header line. \\\cline{2-3} | ||
| & {\tt VN}* & Formate version. \emph{Accepted format}: {\tt /\char94[0-9]+\char92.[0-9]+\$/}.\\\cline{2-3} | ||
| & {\tt SO} & Sorting order. \emph{Valid values}: {\tt unsorted}, {\tt queryname} and {\tt coordinate}. \\\hline | ||
| \multicolumn{2}{|l}{\tt @SQ} & Reference sequence dictionary. \\\cline{2-3} | ||
| & {\tt SN}* & Reference sequence name. Unique among all | ||
| sequence records in the file. The value of this field is used in the | ||
| alignment records. \\\cline{2-3} | ||
| & {\tt LN}* & Reference sequence length. \emph{Range}: {\tt [1,2$^{29}$-1]}\\\cline{2-3} | ||
| & {\tt AS} & Genome assembly identifier. \\\cline{2-3} | ||
| & {\tt M5} & MD5 checksum of the sequence in the uppercase, with gaps and spaces removed.\\\cline{2-3} | ||
| & {\tt SP} & Species.\\\cline{2-3} | ||
| & {\tt UR} & URI of the sequence.\\\hline | ||
| \multicolumn{2}{|l}{\tt @RG} & Read group. \\\cline{2-3} | ||
| & {\tt ID}* & Unique read group identifier. The value of ID | ||
| is used in the RG tags of alignment records. \\\cline{2-3} | ||
| & {\tt CN} & Name of sequencing center producing the read.\\\cline{2-3} | ||
| & {\tt DS} & Description.\\\cline{2-3} | ||
| & {\tt DT} & Date the run was produced (ISO8601 date or date/time).\\\cline{2-3} | ||
| & {\tt LB} & Library.\\\cline{2-3} | ||
| & {\tt PI} & Predicted median insert size.\\\cline{2-3} | ||
| & {\tt PL} & Platform/technology used to produce the read. \emph{Valid values}: | ||
| {\tt ILLUMINA}, {\tt SOLID}, {\tt LS454}, {\tt HELICOS} and {\tt PACBIO}.\\\cline{2-3} | ||
| & {\tt PU} & Platform unit (e.g. lane for Illumina or slide for SOLiD). Unique identifier.\\\cline{2-3} | ||
| & {\tt SM} & Sample. Use pool name where a pool is being sequenced.\\\hline | ||
| \multicolumn{2}{|l}{\tt @PG} & Program. \\\cline{2-3} | ||
| & {\tt ID}* & Program name \\\cline{2-3} | ||
| & {\tt VN} & Program version \\\cline{2-3} | ||
| & {\tt CL} & Command line \\\hline | ||
| \multicolumn{2}{|l}{\tt @CO} & One-line text comment.\\ | ||
| \hline | ||
| \end{tabular} | ||
| \end{center} | ||
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| \subsection{The mandatory fields} | ||
| The following table gives an overview of the mandatory fields in | ||
| the SAM format: | ||
| \begin{center} | ||
| \begin{tabular}{rllll} | ||
| \hline | ||
| {\bf Col} & {\bf Field} & {\bf Type} & {\bf Regexp/Range} & {\bf Brief description} \\ | ||
| \hline | ||
| 1 & {\sf QNAME} & String & {\tt [!-?A-\char126]+} & Query template NAME\\ | ||
| 2 & {\sf FLAG} & Int/Chr & {\tt [0,2$^{16}$-1]}/{\tt [*pPuUrR12sfd]} & bitwise FLAG \\ | ||
| 3 & {\sf RNAME} & String & {\tt [!-\char126]+} & Reference sequence NAME\\ | ||
| 4 & {\sf POS} & Int & {\tt [0,2$^{29}$-1]} & 1-based leftmost mapping POSition \\ | ||
| 5 & {\sf MAPQ} & Int & {\tt [0,2$^8$-1]} & MAPping Quality \\ | ||
| 6 & {\sf CIGAR} & String & {\tt \char92*|([0-9]+[MIDNSHPX=])+} & CIGAR string \\ | ||
| 7 & {\sf RNEXT} & String & {\tt [!-\char126]+} & Ref. name of the mate/next fragment\\ | ||
| 8 & {\sf PNEXT} & Int & {\tt [0,2$^{29}$-1]} & Position of the mate/next fragment \\ | ||
| 9 & {\sf TLEN} & Int & {\tt [0,2$^{29}$-1]} & observed Template LENgth \\ | ||
| 10 & {\sf SEQ} & String & {\tt \char92*|[A-Za-z=]+} & fragment SEQuence\\ | ||
| 11 & {\sf QUAL} & String & {\tt [!-\char126]+} & ASCII of base QUALity+33 \\ | ||
| \hline | ||
| \end{tabular} | ||
| \end{center} | ||
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| \begin{enumerate} | ||
| \item {\sf QNAME}: Query template NAME. Each template has a unique name. | ||
| \item {\sf FLAG}: bitwise FLAG. Each bit is explained in the following | ||
| table: | ||
| \begin{center} | ||
| \begin{tabular}{rcl} | ||
| \hline | ||
| Bit & Char & Description\\ | ||
| \hline | ||
| 0x1 & p & template having multiple fragments in sequencing \\ | ||
| 0x2 & P & each fragment properly aligned according to the aligner \\ | ||
| 0x4 & u & fragment unmapped \\ | ||
| 0x8 & U & next fragment in the template unmapped \\ | ||
| 0x10 & r & {\sf SEQ} being reverse complemented \\ | ||
| 0x20 & R & {\sf SEQ} of the next fragment in the template being reversed \\ | ||
| 0x40 & 1 & the first fragment in the template \\ | ||
| 0x80 & 2 & the last fragment in the template \\ | ||
| 0x100 & s & secondary alignment\\ | ||
| 0x200 & f & not passing quality controls \\ | ||
| 0x400 & d & PCR or optical duplicate \\ | ||
| \hline | ||
| \end{tabular} | ||
| \end{center} | ||
| \begin{itemize} | ||
| \item Bit 0x4 is the only reliable place to tell whether the fragment is unmapped. | ||
| \item If 0x40 and 0x80 are both set, the fragment is part of a linear | ||
| template, but it is neither the first nor the last fragment. If both | ||
| 0x40 and 0x80 are unset, the index of the fragment in the template | ||
| is unknown. This may happen for a non-linear template or the index | ||
| is lost in data processing. | ||
| \item Bit 0x100 marks the alignment not to be used in certain analyses | ||
| when the tools in use are aware of this bit. | ||
| \item \emph{Implicit rules}: if 0x1 is unset, 0x2, 0x8, 0x20, 0x40, | ||
| 0x80 are all regarded to be unset; if 0x4 or 0x8 is set, 0x2 is | ||
| regarded to be unset. | ||
| \item Bits 0x10 and 0x20 only indicate the strand of the | ||
| fragment. Unmapped reads may have these two bits set. | ||
| \end{itemize} | ||
| \item {\sf RNAME}: Reference sequence NAME of the alignment. An unmapped | ||
| fragment without coordinate has a `*' at this field. However, an | ||
| unmapped fragment may also have an ordinary coordinate such that it | ||
| can be placed at a desired position after sorting. | ||
| \item {\sf POS}: 1-based leftmost mapping POSition of the first matching | ||
| base. The first base in a reference sequence has coordinate 1. {\sf | ||
| POS} is set as 0 for an unmapped read without | ||
| coordinate. \emph{Implicit rules}: if {\sf RNAME} is `*', {\sf POS} is | ||
| regarded to be 0, and vice versa. | ||
| \item {\sf MAPQ}: MAPping Quality. It equals | ||
| $-10\log_{10}\Pr\{\mbox{mapping position is wrong}\}$, rounded to the | ||
| nearest integer. | ||
| \item {\sf CIGAR}: CIGAR string. The CIGAR operations are given in the | ||
| following table: | ||
| \begin{center} | ||
| \begin{tabular}{cl} | ||
| \hline | ||
| Op & Description\\ | ||
| \hline | ||
| {\tt M} & alignment match (can be a sequence match or mismatch)\\ | ||
| {\tt I} & insertion to the reference \\ | ||
| {\tt D} & deletion from the reference \\ | ||
| {\tt N} & skipped region from the reference \\ | ||
| {\tt S} & soft clipping (clipped sequences present in {\sf SEQ})\\ | ||
| {\tt H} & hard clipping (clipped sequences NOT present in {\sf SEQ})\\ | ||
| {\tt P} & padding (silent deletion from padded reference)\\ | ||
| {\tt =} & sequence match \\ | ||
| {\tt X} & sequence mismatch \\ | ||
| \hline | ||
| \end{tabular} | ||
| \end{center} | ||
| \begin{itemize} | ||
| \item S/H can only be the first or the last operation. | ||
| \end{itemize} | ||
| \item {\sf RNEXT}: Reference sequence name of the NEXT fragment in the | ||
| template. This field is set as `*' when the information is | ||
| unavailable. | ||
| \item {\sf PNEXT}: Position of the NEXT fragment in the template. Set as | ||
| 0 when the information is unavailable. \emph{Implicit rules}: if {\sf | ||
| RNEXT} is `*', {\sf PNEXT} is regarded to be 0, and vice versa. | ||
| \item {\sf TLEN}: observed Template LENgth. It is set as 0 for | ||
| single-fragment template or when the information is unavailable. | ||
| \item {\sf SEQ}: fragment SEQuence. This field can be a `*' when the | ||
| sequence is not stored. If not a `*', the length of the sequence must | ||
| equal the sum of lengths of M/I/S/=/X operations in {\sf CIGAR}. | ||
| \item {\sf QUAL}: ASCII of base QUALity plus 33. A base quality equals | ||
| $-10\log_{10}\Pr\{\mbox{base is wrong}\}$. This field can be a `*' | ||
| when quality is not stored. If not a `*', {\sf SEQ} is not a `*' and | ||
| the length of the quality string must equal the length of {\sf SEQ}. | ||
| \end{enumerate} | ||
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| \subsection{Optional fields} | ||
| All optional fields can be absent. | ||
| \begin{center} | ||
| \begin{tabular}{ll} | ||
| \hline | ||
| {\bf Tag} & {\bf Description} \\ | ||
| \hline | ||
| \hline | ||
| \end{tabular} | ||
| \end{center} | ||
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| \section{The SAM Format Standards} | ||
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| \end{document} |