sam2mismatch takes a SAM file and uses the CIGAR and MD tag to reconstruct the mismatches of each read.
A C++ compiler, such as G++.
To compile sam2mismatch, enter the src/ directory and type:
make
sam2mismatch can then be moved to /usr/bin/ or wherever is convenient. To remove the compiled files, enter the src/ directory and type:
make clobber
Input can be read out of a SAM file:
sam2mismatch < file.sam > file.tsv
Or from a pipe:
samtools view file.bam | sam2mismatch > file.tsv
To display the current version and quit, enter:
sam2mismatch --version
If you use sam2mismatch in your work, please use the following DOI to cite to original work of sam2pairwise:
