Fetch Data


sra-pileup [options] <accession>


-h | --help Displays ALL options, general usage, and version information.
-V | --version Display the version of the program.
Data formatting:
-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: The file specific reference name (ex: "chr1" or "1"). "from" and "to" are 1-based coordinates.
-q | --minmapq Minimum mapping quality, alignments with a lower mapq will be ignored (default=0).
Workflow and piping:
--option-file Give more options and positions from the file.
-o | --outfile Output will be written to this file instead of std-out.

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