Algorithm 1. Pseudocode of PFA in the GATK HaplotypeCaller.
1: function PFA $H[]$, $R[]$, $Q[]$, $\alpha []$, $\delta []$, $\zeta []$, $m$, $n$
2:  $M\leftarrow 0$ $I\leftarrow 0$ $D\leftarrow 0$
3:  $D_{0,0\dots n}\leftarrow 1/n$
4:  ${\beta }_{0\dots m}\leftarrow 0.9$
5:  ${ϵ}_{0\dots m}\leftarrow 0.1$
6:  for $i\leftarrow \mathrm{1,}m$ do
7:   for $j\leftarrow \mathrm{1,}n$ do
8:    if R [i]==H[j] then
9:     ${\lambda }_{i\mathrm{,}j}\leftarrow Q_i/3$
10:   else
11:     ${\lambda }_{i\mathrm{,}j}\leftarrow 1-Q_i$
12:   end if
13:     $M_{i\mathrm{,}j}\leftarrow {\lambda }_{i\mathrm{,}j}({\alpha }_i{M}_{i-\mathrm{1,}j-1}+{\beta }_i{I}_{i-\mathrm{1,}j-1}+{\beta }_i{D}_{i-\mathrm{1,}j-1})$
14:     $I_{i\mathrm{,}j}\leftarrow {\delta }_i{M}_{i-\mathrm{1,}j}+{ϵ}_i{I}_{i-\mathrm{1,}j}$
15:     $D_{i\mathrm{,}j}\leftarrow {\zeta }_i{M}_{i\mathrm{,}j-1}+{ϵ}_i{D}_{i\mathrm{,}j-1}$
16:   end for
17:  end for
18:  return ${\displaystyle {\sum }_{j=1}^n}(M_{m\mathrm{,}j}+I_{m\mathrm{,}j})$
19: end function