+ -C INT Coefficient to cap mapping quality of poorly mapped
+ reads. See the pileup command for details. [0]
+
+ -r Compute the BQ tag without changing the base quality.
+
+
+ pileup samtools pileup [-2sSBicv] [-f in.ref.fasta] [-t in.ref_list]
+ [-l in.site_list] [-C capMapQ] [-M maxMapQ] [-T theta] [-N
+ nHap] [-r pairDiffRate] [-m mask] [-d maxIndelDepth] [-G
+ indelPrior] <in.bam>|<in.sam>
+
+ Print the alignment in the pileup format. In the pileup for-
+ mat, each line represents a genomic position, consisting of
+ chromosome name, coordinate, reference base, read bases, read
+ qualities and alignment mapping qualities. Information on
+ match, mismatch, indel, strand, mapping quality and start and
+ end of a read are all encoded at the read base column. At
+ this column, a dot stands for a match to the reference base
+ on the forward strand, a comma for a match on the reverse
+ strand, a '>' or '<' for a reference skip, `ACGTN' for a mis-
+ match on the forward strand and `acgtn' for a mismatch on the
+ reverse strand. A pattern `\+[0-9]+[ACGTNacgtn]+' indicates
+ there is an insertion between this reference position and the
+ next reference position. The length of the insertion is given
+ by the integer in the pattern, followed by the inserted
+ sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' repre-
+ sents a deletion from the reference. The deleted bases will
+ be presented as `*' in the following lines. Also at the read
+ base column, a symbol `^' marks the start of a read. The
+ ASCII of the character following `^' minus 33 gives the map-
+ ping quality. A symbol `$' marks the end of a read segment.
+
+ If option -c is applied, the consensus base, Phred-scaled
+ consensus quality, SNP quality (i.e. the Phred-scaled proba-
+ bility of the consensus being identical to the reference) and
+ root mean square (RMS) mapping quality of the reads covering
+ the site will be inserted between the `reference base' and
+ the `read bases' columns. An indel occupies an additional
+ line. Each indel line consists of chromosome name, coordi-
+ nate, a star, the genotype, consensus quality, SNP quality,
+ RMS mapping quality, # covering reads, the first alllele, the
+ second allele, # reads supporting the first allele, # reads
+ supporting the second allele and # reads containing indels
+ different from the top two alleles.
+
+ NOTE: Since 0.1.10, the `pileup' command is deprecated by
+ `mpileup'.
+
+ OPTIONS:
+
+ -B Disable the BAQ computation. See the mpileup com-
+ mand for details.
+
+ -c Call the consensus sequence. Options -T, -N, -I and
+ -r are only effective when -c or -g is in use.
+
+ -C INT Coefficient for downgrading the mapping quality of
+ poorly mapped reads. See the mpileup command for
+ details. [0]
+
+ -d INT Use the first NUM reads in the pileup for indel
+ calling for speed up. Zero for unlimited. [1024]
+
+ -f FILE The reference sequence in the FASTA format. Index
+ file FILE.fai will be created if absent.
+
+ -g Generate genotype likelihood in the binary GLFv3
+ format. This option suppresses -c, -i and -s. This
+ option is deprecated by the mpileup command.
+
+ -i Only output pileup lines containing indels.
+
+ -I INT Phred probability of an indel in sequencing/prep.
+ [40]
+
+ -l FILE List of sites at which pileup is output. This file
+ is space delimited. The first two columns are
+ required to be chromosome and 1-based coordinate.
+ Additional columns are ignored. It is recommended
+ to use option
+
+ -m INT Filter reads with flag containing bits in INT
+ [1796]
+
+ -M INT Cap mapping quality at INT [60]
+
+ -N INT Number of haplotypes in the sample (>=2) [2]
+
+ -r FLOAT Expected fraction of differences between a pair of
+ haplotypes [0.001]
+
+ -s Print the mapping quality as the last column. This
+ option makes the output easier to parse, although
+ this format is not space efficient.
+
+ -S The input file is in SAM.
+
+ -t FILE List of reference names ane sequence lengths, in
+ the format described for the import command. If
+ this option is present, samtools assumes the input
+ <in.alignment> is in SAM format; otherwise it
+ assumes in BAM format. -s together with -l as in
+ the default format we may not know the mapping
+ quality.
+
+ -T FLOAT The theta parameter (error dependency coefficient)
+ in the maq consensus calling model [0.85]
+
projects / samtools.git / blobdiff