From: Identification of pathogen genomic variants through an integrated pipeline
Filtering parameter | Optimized value |
---|---|
Filters tested and found to affect specificity and sensitivity | |
Alignment aggregate mapping quality | <7 |
Total quality | <196.5 |
Depth of coverage | <14 |
Strand bias Fisher’s exact test | >13.5 |
Filters tested and found not to affect specificity and sensitivity | |
Count of nucleotide identity | n/a |
Clipped read significance | n/a |
Depth of coverage per allele | n/a |
Quality by depth | n/a |
Homopolymer run | n/a |
Inbreeding coefficient | n/a |
Allele balance | n/a |
Confidence of elimination of incorrect genotype | n/a |
Root mean square of mapping quality | n/a |
Read position | n/a |
Spanning deletions | n/a |
Reads with mapping quality of zero | n/a |
Reads with a mapping quality of zero | n/a |