GenOO::Data::File::SAM::MDZ - Role - The MD:Z tag in a SAM file
This role when consumed requires specific attributes and provides methods to extract information from the MD:Z tag.
The cigar string does not usually contain information regarding the deletions. For this the MD:Z tag is usually provided. MD:Z -> String for mismatching positions. Regex: [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+) The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string `10A5^AC6' means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string.
# Get the location information on the reference sequence $obj_with_role->mismatch_positions_on_reference_calculated_from_mdz; # (534515, 534529, ...)
To install GenOO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GenOO
CPAN shell
perl -MCPAN -e shell install GenOO
For more information on module installation, please visit the detailed CPAN module installation guide.