Misclassification of FP as TP

[sainsachiko]

I am running hap.py version 0.3.15 and encounter this issue. Some variants are suppose to be FP but they are classified as TP (70k/5mil variants). Have anyone encounter this?

My command is:

/opt/hap.py/bin/hap.py in4276_2_filtered3010.vcf.gz in4328_10_filtered3010.vcf.gz     -r GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta     --threads 20          -o in4328_10_happy_convert     --pass-only     --write-vcf

Thank you for your support.