Coverage quality control
PATHOLOGY
A more detailed notion of each gene percentage, per barcode, covered by at least 100×, in the processed alignments, was also provided using a combination of awk, SAMtools mpileup, BEDtools intersect, multiinter and merge. Bases covered by less than 100× were reported per barcode using the same strategy. Genes belonging to patient pathology were tagged in these two files to facilitate the search for genes of interest that might be badly covered.