sam2tsv
Format
cg sam2tsv ?options? ?infile? ?outfile?
Summary
Converts data in sam format to tsv format.
The original sam header is included in the comments. Extra fields in
the sam file are kept as field:type:value, but put together as a list
in a column named other. Optionally the values for some extra fields
can be split into different columns using the -fields option.
Arguments
- infile
- file to be converted, if not given, uses stdin. File may be
compressed.
- outfile
- write results to outfile, if not given, uses stdout
Options
- -f fields
- list of fields to go in separate columns. The list can eiter
contain just the fieldname, in which case type and description are
taken from a number of known fields. If the field is unknown, type
will be String(Z) and desciption empty. You can also specify type
and field in the list as field:type:description where type is in
the sam format (i,Z,..)
- -addfield field
- add one field to fields; this option can be given multiple
times.
Category
Format Conversion