samtools使用说明书

Program: samtools (Tools for alignments in the SAM format)

Version: 0.1.19-44428cd

Usage: samtools [options]

Command: view SAM<->BAM conversion

sort sort alignment file

mpileup multi-way pileup

depth compute the depth

faidx index/extract FASTA

tview text alignment viewer

index index alignment

idxstats BAM index stats (r595 or later)

fixmate fix mate information

flagstat simple stats

calmd recalculate MD/NM tags and '=' bases

merge merge sorted alignments

rmdup remove PCR duplicates

reheader replace BAM header

cat concatenate BAMs

bedcov read depth per BED region

targetcut cut fosmid regions (for fosmid pool only)

phase phase heterozygotes

bamshuf shuffle and group alignments by name

./samtools view

Usage: samtools view [options] | [region1 [...]]

Options: -b output BAM

-h print header for the SAM output

-H print header only (no alignments)

-S input is SAM

-u uncompressed BAM output (force -b)

-1 fast compression (force -b)

-x output FLAG in HEX (samtools-C specific)

-X output FLAG in string (samtools-C specific)

-c print only the count of matching records

-B collapse the backward CIGAR operation

-@ INT number of BAM compression threads [0]

-L FILE output alignments overlapping the input BED FILE [null]

-t FILE list of reference names and lengths (force -S) [null]

-T FILE reference sequence file (force -S) [null]

-o FILE output file name [stdout]

-R FILE list of read groups to be outputted [null]

-f INT required flag, 0 for unset [0]

-F INT filtering flag, 0 for unset [0]

-q INT minimum mapping quality [0]

-l STR only output reads in library STR [null]

-r STR only output reads in read group STR [null]

-s FLOAT fraction of templates to subsample; integer part as seed [-1]

-? longer help

./samtools sort

Usage: samtools sort [options]

Options: -n sort by read name

-f use as full file name instead of prefix

-o final output to stdout

-l INT compression level, from 0 to 9 [-1]

-@ INT number of sorting and compression threads [1]

-m INT max memory per thread; suffix K/M/G recognized [768M]

./samtools mpileup

Usage: samtools mpileup [options] in1.bam [in2.bam [...]]

Input options:

-6 assume the quality is in the Illumina-1.3+ encoding

-A count anomalous read pairs

-B disable BAQ computation

-b FILE list of input BAM filenames, one per line [null]

-C INT parameter for adjusting mapQ; 0 to disable [0]

-d INT max per-BAM depth to avoid excessive memory usage [250]

-E recalculate extended BAQ on the fly thus ignoring existing BQs -f FILE faidx indexed reference sequence file [null]

-G FILE exclude read groups listed in FILE [null]

-l FILE list of positions (chr pos) or regions (BED) [null]

-M INT cap mapping quality at INT [60]

-r STR region in which pileup is generated [null]

-R ignore RG tags

-q INT skip alignments with mapQ smaller than INT [0]

-Q INT skip bases with baseQ/BAQ smaller than INT [13]

--rf INT required flags: skip reads with mask bits unset []

--ff INT filter flags: skip reads with mask bits set []

Output options:

-D output per-sample DP in BCF (require -g/-u)

-g generate BCF output (genotype likelihoods)

-O output base positions on reads (disabled by -g/-u)

-s output mapping quality (disabled by -g/-u)

-S output per-sample strand bias P-value in BCF (require -g/-u)

-u generate uncompress BCF output

SNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):

-e INT Phred-scaled gap extension seq error probability [20]

-F FLOAT minimum fraction of gapped reads for candidates [0.002]

-h INT coefficient for homopolymer errors [100]

-I do not perform indel calling

-L INT max per-sample depth for INDEL calling [250]

-m INT minimum gapped reads for indel candidates [1]

-o INT Phred-scaled gap open sequencing error probability [40]

-p apply -m and -F per-sample to increase sensitivity

-P STR comma separated list of platforms for indels [all]

Notes: Assuming diploid individuals.

./samtools depth

Usage: samtools depth [options] in1.bam [in2.bam [...]]

Options:

-b list of positions or regions

-f list of input BAM filenames, one per line [null]

-l minQLen

-q base quality threshold

-Q mapping quality threshold

-r region

./samtools faidx

Usage: faidx [ [...]]

./samtools tview

Usage: bamtk tview [options] [ref.fasta]

Options:

-d display output as (H)tml or (C)urses or (T)ext

-p chr:pos go directly to this position

-s STR display only reads from this sample or group

Usage: samtools index [out.index]

./samtools idxstats

Usage: samtools idxstats

./samtools fixmate

Usage: samtools fixmate

Options:

-r remove unmapped reads and secondary alignments

./samtools flagstat

Usage: samtools flagstat

./samtools calmd

Usage: samtools fillmd [-eubrS]

Options: -e change identical bases to '='

-u uncompressed BAM output (for piping)

-b compressed BAM output

-S the input is SAM with header

-A modify the quality string

-r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)

-E extended BAQ for better sensitivity but lower specificity Usage: samtools merge [-nr] [-h inh.sam] [...]

Options: -n sort by read names

-r attach RG tag (inferred from file names)

-u uncompressed BAM output

-f overwrite the output BAM if exist

-1 compress level 1

-l INT compression level, from 0 to 9 [-1]

-@ INT number of BAM compression threads [0]

-R STR merge file in the specified region STR [all]

-h FILE copy the header in FILE to [in1.bam]

Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users must provide the correct header with -h, or uses Picard which properly maintains the header dictionary in merging.

Usage: samtools rmdup [-sS]

Option: -s rmdup for SE reads

-S treat PE reads as SE in rmdup (force -s)

./samtools reheader

Usage: samtools reheader

./samtools cat

Usage: samtools cat [-h header.sam] [-o out.bam] [...]

./samtools bedcov

Usage: samtools bedcov [...]

./samtools targetcut

Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] ./samtools phase

Usage: samtools phase [options]

Options: -k INT block length [13]

-b STR prefix of BAMs to output [null]

-q INT min het phred-LOD [37]

-Q INT min base quality in het calling [13]

-D INT max read depth [256]

-F do not attempt to fix chimeras

-A drop reads with ambiguous phase

./samtools bamshuf

Usage: bamshuf [-Ou] [-n nFiles] [-c cLevel]

Options: -O output to stdout

-u uncompressed BAM output

-l INT compression level [1]

-n INT number of temporary files [64]