Fetch Data


sam-dump [options] <path/file> [<path/file> ...]


This tool is part of NCBI's SRA toolkit.

Convert SRA data to SAM format. If the orignal submitter sends both the fastq file and aligned sam file to the NCBI SRA database, sam-dump can download the aligned sam file; however, if the submitter doesn't upload the aligned sam file, sam-dump exports an unaligned SAM, which may not be directly used in downstream analysis. In this case, you may want to dump fastq files with fasterq-dump first, then perform the alignment on your own machines.

Required arguments

  • path: Path to a .sra file


  • -u, --unaligned: Output unaligned reads along with aligned reads
  • -1, --primary: Output only primary alignments
  • --aligned-region <name[:from-to]>: Filter by position on genome. Name can either be file specific name (ex: chr1 or 1). from and to (inclusive) are 1-based coordinates
  • --matepair-distance <from-to|'unknown'>: Filter by distance between matepairs. Use "unknown" to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference
  • --min-mapq: minimum mapping quality an alignment has to have, to be printed
Data formatting
  • -s, --seqid: Print reference SEQ_ID in RNAME instead of NAME
  • -c, --cigar-long: Output long version of CIGAR
  • --cigar-CG: Output CG version of CIGAR
  • -r, --header: Always reconstruct header
  • --header-file <filename>: take all headers from this file
  • -n, --no-header: Do not output headers
  • --header-comment <text>: Add comment to header. Use multiple times for several lines. Use quotes
  • -=, --hide-identical: Output '=' if base is identical to reference
  • --gzip: Compress output using gzip
  • --bzip2: Compress output using bzip2
  • -g, --spot-group: Add .SPOT_GROUP to QNAME
  • --fastq: Produce FastQ formatted output
  • --fasta: Produce Fasta formatted output
  • -p <prefix>, --prefix <prefix>: Prefix QNAME: prefix.QNAME
  • --reverse: Reverse unaligned reads according to read type
  • --cigar-CG-merge: Apply CG fixups to CIGAR/SEQ/QUAL and outputs CG-specific columns
  • --XI: Output cSRA alignment id in XI column
  • -Q <quantization string>, --qual-quant <quantization string>: Quality scores quantization level string like '1:10,10:20,20:30,30:-'
  • --CG-evidence: Output CG evidence aligned to reference
  • --CG-ev-dnb: Output CG evidence DNB's aligned to evidence
  • --CG-mappings: Output CG sequences aligned to reference
  • --CG-SAM: Output CG evidence DNB's aligned to reference
  • --report: report options instead of executing
  • --output-file: print output into this file (instead of STDOUT)
  • --output-buffer-size: size of output-buffer(default:32k,
  • --cachereport: print report about mate-pair-cache
  • --unaligned-spots-only: output reads for spots with no aligned reads
  • --CG-names: prints cg-style spotgroup.spotid formed names
  • --cursor-cache: open cached cursor with this size
  • --no-mate-cache: do not use mate-cache, slower but less memory usage
  • --rna-splicing: modify cigar-string (replace .D. with .N.) and add output flags (XS:A:+/-) when rna-splicing is detected by match to spliceosome recognition sites
  • --rna-splice-level: level of rna-splicing detection (0,1,2) when testing for spliceosome recognition sites
    • 0=perfect match
    • 1=one mismatch
    • 2=two mismatches one on each site
  • --rna-splice-log: file, into which rna-splice events are written
  • --with-md-flag: print MD-flag
General options
  • --disable-multithreading: disable multithreading
  • -h, --help: Output brief explanation for the program.
  • -V, --version: Display the version of the program then quit.
  • -L <level>, --log-level <level>: Logging level as number or enum string. One of (fatal|sys|int|err|warn|info|debug) or (0-6). Current/default is warn.
  • -v, --verbose: Increase the verbosity of the program status messages. Use multiple times for more verbosity. Negates quiet.
  • -q, --quiet: Turn off all status messages for the program. Negated by verbose.
  • --option-file <file>: Read more options and parameters from the file.

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