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Table 2 Optimized filtering parameters applied by Platypus

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

  1. The final set of optimized filtering parameters evaluated by the searching algorithm. The set of informative filters gives 90% sensitivity with a specificity of 86%.