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Tag alignment files (version 0.5.25)

tag_file:

Alignments

Alignments 0

Reference fasta for realigning clipped reads:

This file is optional. If you provide it, clipped sequences are extracted and aligned against this fasta file.

Allow dovetailing:

Check this to label reads as proper_pair even if the mates of a pair overlap each other

Discard suboptimal alternative tags:

Check this to discard alternative tags that cannot explain the current read cigar

Discard alternative tags for proper pairs:

Check this to discard alternative tags for reads in proper pairs

Check this to produce an output file containing only the reads with tags that failed validation:

Check this to produce an output file containing only the reads with tags that pass validation:

usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o
                  OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED]
                  [-wv WRITE_VERIFIED] [--version]

Tag reads in an alignment file based on other alignment files

optional arguments:
  -h, --help            show this help message and exit
  -t TAG_FILE, --tag_file TAG_FILE
                        Tag reads in this file. (default: None)
  -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...]
                        Tag reads in readfile if reads are aligned in these
                        files.Append `:A:B` to tag first letter of tag
                        describing read as A, and first letter of tag
                        describing the mate as B (default: None)
  -o OUTPUT_FILE, --output_file OUTPUT_FILE
                        Write bam file to this path (default: None)
  -d, --allow_dovetailing
                        Sets the proper pair flag (0x0002) to true if reads
                        dovetail [reads reach into or surpass the mate
                        sequence]. (default: False)
  -dp, --discard_if_proper_pair
                        Discard an alternative flag if the current read is in
                        a proper pair. (default: False)
  -k, --keep_suboptimal_alternate_tags
                        By default cigarstrings of the alternative tags are
                        compared and alternates that are not explaining the
                        current cigar strings are discarded. Use this option
                        to keep the alternative tags (effectively restoring
                        the behaviour of readtagger < 0.1.4) (default: False)
  -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED
                        Write discarded reads into separate file (default:
                        False)
  -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED
                        Write verified reads into separate file (default:
                        False)
  --version             show program's version number and exit