lapels 1.1.1

Lapels remaps reads aligned to the in silico genome back to the reference coordinate and annotates variants.

Two files are taken as input:

1. a MOD file that is used to generate the in silico genome and

2. a BAM file that contains the in silico genome alignments.

Lapels will generate a new BAM file with corrected read positions, adjusted cigar strings, and annotated tags of variants (eg. SNPs, Insertions, and Deletions).