Fraction of reads mapping to the human genome
Ensure there is adequate mapping of sequenced reads to the human genome
Theoretical Method
This metric is obtained by iterating through the bam file, and looking at the sam flag which indicates whether each read has an adequate mapping to the HG19 reference.
Technical Methods
Waltz uses a method from the of the HTSJDK library:
Interpretations
Mapping fraction to the human genome should be above 97%, in most cases if it is below that, there is a chance that there is contamination from another species.
