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:
- a MOD file that is used to generate the in silico genome and
- 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).
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