SRA Toolkit DocumentationBack to List of the Tools
sra-pileup [options] <path/file> [<path/file> ...]
sra-pileup [options] <accession>
Frequently Used Options:
|-h|||||--help||Displays ALL options, general usage, and version information.|
|-V|||||--version||Display the version of the program.|
|-e|||||--seqname||Use the original sequence-names (ex: chr1) instead of matching accessions.|
|--function count||Sorted output with per-base counters (name, position, reference base, read depth, # of matches to reference, # of calls for each non-reference base, insertions, deletions, strand %).|
|--function mismatch||Output only lines with a mismatch.|
|--minmismatch||Minimum percent of mismatches used as the cutoff in “--function mismatch” (default is 5).|
|--function ref||List the references used in the file.|
|-r|||||--aligned-region||Filter by position on genome <name[:from-to]>. Name: The file specific reference name (ex: "chr1" or "1"). "from" and "to" are 1-based coordinates.|
|-q|||||--minmapq <min. mapq>||Minimum mapping quality, alignments with a lower mapq will be ignored (default=0).|
|Workflow and piping:|
|--option-file <file>||Give more options and positions from the file.|
|-o|||||--outfile <output-file>||Output will be written to this file instead of std-out.|
Produces pileup stats for a given genomic region (-r), chromosome 1, bases 559140-559160 (1:559140-559160).
sra-pileup -r 1:559140-559160 SRR390728
Writes pileup stats to a file called "output.txt" (-o output.txt) that is gzipped (--gzip), from a list of positions contained in the file "list.txt" (--option-file list.txt). The format of "list.txt" is:
sra-pileup -o output.txt --gzip --option-file list.txt SRR390728
- -r 1:559140-559141
- -r 1:569145-569145
- -r 1:579150-579150
Produces pileup stats using the original sequence names (-e) and only for positions with a mismatch (--function mismatch) and at least 1% of reads are mismatched at that position (--minmismatch 1) for a given genomic region (-r), chromosome 1, bases 559140-559160 (1:559140-559160). Output columns are: reference sequence, 1-based position, coverage, number of mismatches
sra-pileup -e --function mismatch --minmismatch 1 -r 1:559140-559160 SRR390728
Produces a per-base count (--function count) for a given genomic region (-r), chromosome 10, bases 143076-143080 (chr10:143076-143080) with output columns: seq-name, genomic-coordinate, reference base, read depth at position, # of reads that match reference, # of calls for each non-reference base, insertions, deletions, % of reads on forward strand.
sra-pileup --function count -r chr10:143076-143080 SRR944105
Possible errors and their solution:
The tool is unable to resolve the base position or list of positions, check for typos, formatting errors and path to the option-file. Note that the chromosome name needs to match what was used in the originally submitted file (1 vs. chr1 for instance), this command will work:
item not found while searching type within alignment module - ReferenceList_Find() failed
sra-pileup -r 1:559140-559160 -o pilestat.txt SRR390728But this command will cause an error:
sra-pileup -r chr1:559140-559160 -o pilestat.txt SRR390728Reference names can be found by running SRA stat and looking for the "name=" under <AlignInfo>:
sra-stat -x -q SRR390728
This error indicates that the .sra file cannot be found. Confirm that the path to the file is correct.
directory not found while opening manager within virtual file system module - failed to open "SRR*"
This error indicates that the specified Run was not submitted as aligned data. Only data submitted as aligned (ie: bam format) can be analyzed by sra-pileup.
item unsupported while opening within application support module - failed to open "SRR*", it is not a vdb-database
This error indicates an unrecognized argument. Check your command line for typos, the problem option is usually indicated in quotes at the end of the error message.
param unknown while parsing argument list within application support module - Unknown argument