lapels 1.1.1

Lapels - A remapper and annotator of in silico (pseudo) genome alignments

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).