samtools mpileup [-EB] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]
Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.
Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file.
Several columns contain numeric quality values encoded as individual ASCII characters. Each character can range from “!” to “~” and is decoded by taking its ASCII value and subtracting 33; e.g., “A” encodes the numeric value 32.
The first three columns give the position and reference:
The remaining columns show the pileup data, and are repeated for each input BAM file specified:
For each read covering the position, this column contains:
|. dot||, comma||Base matches the reference base|
|ACGTN||acgtn||Base is a mismatch to the reference base|
|>||<||Reference skip (due to CIGAR “N”)|
|*||*/#||Deletion of the reference base (CIGAR “D”)|
Deleted bases are shown as “*” on both strands unless --reverse-del is used, in which case they are shown as “#” on the reverse strand.
Any output column that would be empty, such as a tag which is not present or the filtered sequence depth is zero, is reported as "*". This ensures a consistent number of columns across all reported positions.
Assume the quality is in the Illumina 1.3+ encoding.
Do not skip anomalous read pairs in variant calling. Anomalous read pairs are those marked in the FLAG field as paired in sequencing but without the properly-paired flag set.
List of input BAM files, one file per line [null]
Disable base alignment quality (BAQ) computation. See BAQ below.
Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. 
At a position, read maximally INT reads per input file. Setting this limit reduces the amount of memory and time needed to process regions with very high coverage. Passing zero for this option sets it to the highest possible value, effectively removing the depth limit. 
Note that up to release 1.8, samtools would enforce a minimum value for this option. This no longer happens and the limit is set exactly as specified.
Recalculate BAQ on the fly, ignore existing BQ tags. See BAQ below.
The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by bgzip. [null]
Supplying a reference file will enable base alignment quality calculation for all reads aligned to a reference in the file. See BAQ below.
Exclude reads from read groups listed in FILE (one @RG-ID per line)
BED or position list file containing a list of regions or sites where
pileup or BCF should be generated. Position list files contain two
columns (chromosome and position) and start counting from 1. BED
files contain at least 3 columns (chromosome, start and end position)
and are 0-based half-open.
While it is possible to mix both position-list and BED coordinates in the same file, this is strongly ill advised due to the differing coordinate systems. [null]
Minimum mapping quality for an alignment to be used 
Minimum base quality for a base to be considered. 
Note base-quality 0 is used as a filtering mechanism for overlap removal which marks bases as having quality zero and lets the base quality filter remove them. Hence using --min-BQ 0 will make the overlapping bases reappear, albeit with quality zero.
Only generate pileup in region. Requires the BAM files to be indexed. If used in conjunction with -l then considers the intersection of the two requests. STR [all sites]
Ignore RG tags. Treat all reads in one BAM as one sample.
Required flags: include reads with any of the mask bits set [null]
Filter flags: skip reads with any of the mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
Overlap detection and removal is enabled by default. This option turns it off.
When enabled, where the ends of a read-pair overlap the overlapping region will have one base selected and the duplicate base nullified by setting its phred score to zero. It will then be discarded by the --min-BQ option unless this is zero.
The quality values of the retained base within an overlap will be the summation of the two bases if they agree, or 0.8 times the higher of the two bases if they disagree, with the base nucleotide also being the higher confident call.
Include customized index file as a part of arguments. See EXAMPLES section for sample of usage.
Write pileup output to FILE, rather than the default of standard output.
Output base positions on reads in orientation listed in the SAM file (left to right).
Output base positions on reads in their original 5' to 3' orientation.
Output mapping qualities encoded as ASCII characters.
Output an extra column containing comma-separated read names. Equivalent to --output-extra QNAME.
Output extra columns containing comma-separated values of read fields or read tags. The names of the selected fields have to be provided as they are described in the SAM Specification (pag. 6) and will be output by the mpileup command in the same order as in the document (i.e. QNAME, FLAG, RNAME,...) The names are case sensitive. Currently, only the following fields are supported:
QNAME, FLAG, RNAME, POS, MAPQ, RNEXT, PNEXT
Anything that is not on this list is treated as a potential tag, although only two character tags are accepted. In the mpileup output, tag columns are displayed in the order they were provided by the user in the command line. Field and tag names have to be provided in a comma-separated string to the mpileup command. Tags with type B (byte array) type are not supported. An absent or unsupported tag will be listed as "*". E.g.
samtools mpileup --output-extra FLAG,QNAME,RG,NM in.bam
will display four extra columns in the mpileup output, the first being a list of comma-separated read names, followed by a list of flag values, a list of RG tag values and a list of NM tag values. Field values are always displayed before tag values.
Specify a different separator character for tag value lists, when those values might contain one or more commas (,), which is the default list separator. This option only affects columns for two-letter tags like NM; standard fields like FLAG or QNAME will always be separated by commas.
Specify a different 'no value' character for tag list entries corresponding to reads that don't have a tag requested with the --output-extra option. The default is *.
This option only applies to rows that have at least one read in the pileup, and only to columns for two-letter tags. Columns for empty rows will always be printed as *.
Adds base modification markup into the sequence column. This uses the Mm and Ml auxiliary tags (or their uppercase equivalents). Any base in the sequence output may be followed by a series of strand code quality strings enclosed within square brackets where strand is "+" or "-", code is a single character (such as "m" or "h") or a ChEBI numeric in parentheses, and quality is an optional numeric quality value. For example a "C" base with possible 5mC and 5hmC base modification may be reported as "C[+m179+h40]".
Quality values are from 0 to 255 inclusive, representing a linear scale of probability 0.0 to 1.0 in 1/256ths increments. If quality values are absent (no Ml tag) these are omitted, giving an example string of "C[+m+h]".
Note the base modifications may be identified on the reverse strand, either due to the native ability for this detection by the sequencing instrument or by the sequence subsequently being reverse complemented. This can lead to modification codes, such as "m" meaning 5mC, being shown for their complementary bases, such as "G[-m50]".
When --output-mods is selected base modifications can appear on any base in the sequence output, including during insertions. This may make parsing the string more complex, so also see the --no-output-ins-mods and --no-output-ins options to simplify this process.
Do not output the inserted bases in the sequence column. Usually this is reported as "+length sequence", but with this option it becomes simply "+length". For example an insertion of AGT in a pileup column changes from "CCC+3AGTGCC" to "CCC+3GCC".
Specifying this option twice also removes the "+length" portion, changing the example above to "CCCGCC".
The purpose of this change is to simplify parsing using basic regular expressions, which traditionally cannot perform counting operations. It is particularly beneficial when used in conjunction with --output-mods as the syntax of the inserted sequence is adjusted to also report possible base modifications, but see also --no-output-ins-mods as an alternative.
Outputs the inserted bases in the sequence, but excluding any base modifications. This only affects output when --output-mods is also used.
Do not output deleted reference bases in the sequence column. Normally this is reported as "+length sequence", but with this option it becomes simply "+length". For example an deletion of 3 unknown bases (due to no reference being specified) would normally be seen in a column as e.g. "CCC-3NNNGCC", but will be reported as "CCC-3GCC" with this option.
Specifying this option twice also removes the "-length" portion, changing the example above to "CCCGCC".
The purpose of this change is to simplify parsing using basic regular expressions, which traditionally cannot perform counting operations. See also --no-output-ins.
Removes the “^” (with mapping quality) and “$” markup from the sequence column.
Mark the deletions on the reverse strand with the character #, instead of the usual *.
Output all positions, including those with zero depth.
Output absolutely all positions, including unused reference sequences. Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.
BAQ (Base Alignment Quality)
BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8 <https://doi.org/10.1093/bioinformatics/btr076>
BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option.
It is possible to store precalculated BAQ values in a SAM BQ:Z tag. Samtools mpileup will use the precalculated values if it finds them. The -E option can be used to make it ignore the contents of the BQ:Z tag and force it to recalculate the BAQ scores by making a new alignment.
Written by Heng Li from the Sanger Institute.
samtools (1), samtools-depth (1), samtools-sort (1), bcftools (1)
Samtools website: <http://www.htslib.org/>
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