Variant Analysis


samtools mpileup [-EBugp] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]


-6, --illumina1.3+
Assume the quality is in the Illumina 1.3+ encoding.
-A, --count-orphans
Do not skip anomalous read pairs in variant calling.
-b, --bam-list FILE
List of input BAM files, one file per line [null]
-B, --no-BAQ
Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
-C, --adjust-MQ INT
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. [0]
-d, --max-depth INT
At a position, read maximally INT reads per input file. Note that samtools has a minimum value of 8000/n where n is the number of input files given to mpileup. This means the default is highly likely to be increased. Once above the cross-sample minimum of 8000 the -d parameter will have an effect. [250]
-E, --redo-BAQ
Recalculate BAQ on the fly, ignore existing BQ tags
-f, --fasta-ref FILE
The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by bgzip. [null]
-G, --exclude-RG FILE
Exclude reads from readgroups listed in FILE (one @RG-ID per line)
-l, --positions FILE
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]
-q, -min-MQ INT
Minimum mapping quality for an alignment to be used [0]
-Q, --min-BQ INT
Minimum base quality for a base to be considered [13]
-r, --region STR
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]
-R, --ignore-RG
Ignore RG tags. Treat all reads in one BAM as one sample.
--rf, --incl-flags STR|INT
Required flags: skip reads with mask bits unset [null]
--ff, --excl-flags STR|INT
Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
-x, --ignore-overlaps
Disable read-pair overlap detection.
-o, --output FILE
Write pileup or VCF/BCF output to FILE, rather than the default of standard output. (The same short option is used for both --open-prob and --output. If -o's argument contains any non-digit characters other than a leading + or - sign, it is interpreted as --output. Usually the filename extension will take care of this, but to write to an entirely numeric filename use -o ./123 or --output 123.)
-g, --BCF
Compute genotype likelihoods and output them in the binary call format (BCF). As of v1.0, this is BCF2 which is incompatible with the BCF1 format produced by previous (0.1.x) versions of samtools.
-v, --VCF
Compute genotype likelihoods and output them in the variant call format (VCF). Output is bgzip-compressed VCF unless -u option is set.
-O, --output-BP
Output base positions on reads.
-s, --output-MQ
Output mapping quality.
Output per-sample read depth [DEPRECATED - use -t DP instead]
Output per-sample Phred-scaled strand bias P-value [DEPRECATED - use -t SP instead]
-t, --output-tags LIST
Comma-separated list of FORMAT and INFO tags to output (case-insensitive): AD (Allelic depth, FORMAT), INFO/AD (Total allelic depth, INFO), ADF (Allelic depths on the forward strand, FORMAT), INFO/ADF (Total allelic depths on the forward strand, INFO), ADR (Allelic depths on the reverse strand, FORMAT), INFO/ADR (Total allelic depths on the reverse strand, INFO), DP (Number of high-quality bases, FORMAT), DV (Deprecated in favor of AD; Number of high-quality non-reference bases, FORMAT), DPR (Deprecated in favor of AD; Number of high-quality bases for each observed allele, FORMAT), INFO/DPR (Number of high-quality bases for each observed allele, INFO), DP4 (Deprecated in favor of ADF and ADR; Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases, FORMAT), SP (Phred-scaled strand bias P-value, FORMAT) [null]
-u, --uncompressed
Generate uncompressed VCF/BCF output, which is preferred for piping.
Output per-sample number of non-reference reads [DEPRECATED - use -t DV instead]
-e, --ext-prob INT
Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20]
-F, --gap-frac FLOAT
Minimum fraction of gapped reads [0.002]
-h, --tandem-qual INT
Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. [100]
-I, --skip-indels
Do not perform INDEL calling
-L, --max-idepth INT
Skip INDEL calling if the average per-input-file depth is above INT. [250]
-m, --min-ireads INT
Minimum number gapped reads for indel candidates INT. [1]
-o, --open-prob INT
Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. [40] (The same short option is used for both --open-prob and --output. When -o's argument contains only an optional + or - sign followed by the digits 0 to 9, it is interpreted as --open-prob.)
-p, --per-sample-mF
Apply -m and -F thresholds per sample to increase sensitivity of calling. By default both options are applied to reads pooled from all samples.
-P, --platforms STR
Comma-delimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA. [all]

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