sra-pileup [options] <accession>
General: | ||||
-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. | |||
Filtering: | ||||
-r | | | --aligned-region |
Filter by position on genome |
|
-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. |