Stampy-Sapelo2old
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[Category:Sapelo2old]]
Category
Bioinformatics
Program On
Sapelo2
Version
1.0.31
Author / Distributor
Please see https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/stampy
Description
From https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/stampy: "Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq."
Running Program
Also refer to Running Jobs on Sapelo2
For more information on Environment Modules on Sapelo2 please see the Lmod page.
- Version 1.0.31, installed in /usr/local/apps/eb/Stampy/1.0.31-foss-2016b-Python-2.7.14
To use this version of Stampy, please first load the module with
module load Stampy/1.0.31-foss-2016b-Python-2.7.14
This module will automatically load Python/2.7.14-foss-2016b and other dependencies.
Sample job submission script (sub.sh) to run stampy.py:
#PBS -S /bin/bash #PBS -q batch #PBS -N jobname #PBS -l nodes=1:ppn=1 #PBS -l walltime=4:00:00 #PBS -l mem=2gb cd $PBS_O_WORKDIR module load Stampy/1.0.31-foss-2016b-Python-2.7.14 stampy.py [options]
where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.
Submit the job to the queue with
qsub sub.sh
Documentation
See for example https://www.well.ox.ac.uk/files-library/readme.txt
module load Stampy/1.0.31-foss-2016b-Python-2.7.14 stampy.py --help stampy v1.0.31 (r3759), <gerton.lunter@well.ox.ac.uk> Usage: /usr/local/apps/eb/Stampy/1.0.31-foss-2016b-Python-2.7.14/stampy.py [options] [files] Command options (one required) -G PREFIX, --build-genome=PREFIX Build genome index PREFIX.stidx from fasta file(s) on command line -H PREFIX, --build-hash=PREFIX Build hash PREFIX.sthash -M FILE, --map=FILE[,FILE] Map fastq/fasta/BAM file(s) -S FILE, --simulate=FILE Simulate reads following empirical qualities from read FILE -P FILE, --parse=FILE Parse simulated SAM file, and report statistics -A FILE Convert qualities; strip adapters Mapping options: -g PREFIX, --genome=PREFIX Use genome index file PREFIX.stidx -h PREFIX, --hash=PREFIX Use hash file PREFIX.sthash -t N, --threads=N Number of threads to use [1] --numrecords=N Number of records to process [all] --processpart=A/B Process the Ath read (pair) in every block of B read (pairs) [1/1] --minposterior=N Minimum read mapping phred posterior [no filtering] --maxscore=N Maximum read likelihood phred score [no filtering] --qualitybase=C Character or ASCII for quality score 0 in input [33 or !] --logit Qualities are logit (log p/1-p) rather than phred (log p) scores [phred] --solexa, --solexaold, --sanger Short for: --qualitybase=@; --qualitybase=@ --logit; default --substitutionrate=F Set substitution rate for mapping and simulation [0.001] --gapopen=N Gap open penalty (phred score) [40] --gapextend=N Gap extension penalty (phred score) [3] --insertsize=N (Initial) mean insert size for paired-end reads [250] --insertsd=N (Initial) standard deviation for insert size [60] --insertsize2=N (Initial) mean insert size for mate pairs [-2000] --insertsd2=N (Initial) standard deviation for mate pairs [-1 = deactivated] --maxpairseeds=N Number of ambiguous single mappings to take forward for paired realignment [25] --noautosense Do not auto-sense insert size distribution(s) [False] --sensitive More sensitive; about 25-50% slower --fast Less sensitive; about 50% (paired-end) to 100% (single-ended) faster --bwaoptions=opts Options and <prefix> for BWA pre-mapper (quote multiple options) --bwamaxmismatch=N Max number of mismatches for BWA maps; -1=auto [-1] --bwatmpdir=S Set directory for BWA temporary files --bwa=F Set BWA executable [default: bwa] --bwamark Include/mark BWA-mapped reads with XP:Z:BWA tag (produces more output lines) Output options: -o FILE, --output=FILE Write mapping output to FILE [stdout] -f FMT, --outputformat=FMT Select mapping output format (sam,maqtxt,maqmap,maqmapN) [sam] --rightmost Flush gaps to rightmost position in reference coordinates [leftmost] --xa-max Number of alternative hits to output for single/concordant paired reads [0, max 20] --xa-max-discordant Number of alternative hits to output for discordant paired reads [0] --overwrite Allow overwriting of output files --baq (SAM format) Compute base-alignment quality (BAQ; BQ tag) --alignquals (SAM format) Compute posterior alignment probabilities (YQ tag) --xcigar (SAM format) Compute the extended CIGAR string (XC tag) --readgroup=ID:id,tag:value,... (SAM format) Set readgroup tags (ID,SM,LB,DS,PU,PI,CN,DT,PL); ",," quotes "," --norefoutput (SAM format) Use = signs at read positions that match the reference --comment=comment1%comment2%... (SAM format) Add @COmments. % separate lines; commas are converted into tabs --comment=@F (SAM format) Add @COmments from file F Simulation options (use with -S): --seed=N Set random number seed [1] --simulate-minindellen=N Minimum indel length to simulate; negative is deletion [0] --simulate-maxindellen=N Maximum indel length to simulate; negative is deletion [0] --simulate-duplications For insertions, simulate duplications rather than (default) random sequence insertion --simulate-numsubstitutions=N Insert N substitutions in read (pairs) (default = Poisson distribution) Advanced options: --maxcount=N (-H) Maximum multiplicity of repeat words [200] --assembly=S (-G) Set assembly identifier (appears in @SQ field (AS tag) in SAM output) --species=S (-G) Set species identifier (appears in @SQ field (SP tag) in SAM output) --referenceuri=S (-G) Set URI for the reference (appears in @SQ field (UR tag) in SAM output) --noparseNCBI (-G) Don't parse but just copy gi|nnn|ref|xxx| labels in NCBI fasta files --strip-adapter (-A) Strip adapters from fastq files --inputformat=FMT Read input format (fasta, fastq, sam, bam) [fastq] --banding=N Band size for banded alignment; -1=none [60] --fastaqual=N Base quality for fasta input [30] --maxbasequal=N Maximum accepted base quality [50] --svprior=N Prior probability of read pair bridging a SV (phred score) [55] --longindelprior=N Prior probability of read pair bridging a long indel (phred score) [40] --baseentropy=N Entropy of inserted nucleotides (phred score) [5] --remote=U Command to get input reads from URL %s; shortcuts are 'wget' and 'scp' --keepreforder (-M) (default) Use reference order in .fa/.stidx file, rather than alphabetical --alphabetical (-M) Order reference identifiers alphabetically --labelfilter=R (-M) Only map reads / read pairs whose label match the regular expression R --casava8 (-M) Parse Casava v1.8 FastQ headers; include but do not map filtered reads --separator1=c (-M) Use 'c' as separator for Casava data columns [:] --separator2=c (-M) use 'c' as separator between first 7 columns, and the auxiliary columns [ ] --gatkcigarworkaround (-M) Remove adjacent I/D CIGAR operators (valid in SAM spec, but trips up GATK) --unclipq (-M X.bam / -M --bamoptions) Undo soft clipping over low Q bases (-1=disable) [10] --bamsortprefix=S (-M X.bam) Temporary storage for sorting [--output argument, or /tmp/bamsort] --bamsortbuflen=N (-M X.bam) Entries in memory sort buffer [10000] --bamsortmemory=N (-M X.bam) Value for option -m to samtools sort [200000000] (samtools 1.3: 200M) --bamkeepgoodreads (-M X.bam) If set, do not re-map already well-mapped reads from BAM [False] General options: -?, --help Display this help page -v N, --verbosity=N Set verbosity level to N [2] --logfile=FILE Send logging information to FILE [stderr]
Installation
- Version 1.0.31 downloaded from https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/stampy
System
64-bit Linux