Table 1 Features used in the logistic regression model

DP

NGS read depth at the variant position.

78–433 (222)

AD

Number of reads that support the variant call.

25–393 (110)

AF

Fraction of reads that support the variant call, i.e. AD / DP.

0.13–0.56 (0.49)

GC @ 5, 20, 50

Fraction of GC content in the 5, 20, and 50 bases around the variant position.

0.18–0.73 (0.45)

0.29–0.69 (0.44)

0.30–0.68 (0.42)

MQ

Root Mean Square of the mapping quality of the call.

59.3–60 (60)

GQ

Genotype Quality of the call.

50–99 (99)

WHR

Weighted Homopolymer Rate in a window of 20 bases around the variant position: the sum of squares of the homopolymer lengths, divided by the number of homopolymers.

1.6–4.3 (2.4)

HPL-D

Distance to the longest homopolymer within 20 bases from the call position.

0–15 (5)

HPL-L

Length of the longest homopolymer within 20 bases from the call position.

2–6 (4)

QUAL

Quality score assigned by the GATK HaplotypeCaller to the call.

142–5448 (2564)

QD

QUAL, normalized by DP.

1.6–16.9 (11.3)

FS

Phred-scaled p-value using Fisher’s exact test, to detect strand bias.

0–9.2 (1.7)