Arang Rhie

FP in phased variant overlapping non-phased variant

3

Hello, It seems like hap.py does not properly handle phased variants that overlap with non-phased variants. Here is an example: ``` chr20 55234351 . A T 500 PASS AC=1;AF=0.5;AN=2;DA=39;DP=78;GM=1;MC=0;MF=0;MQ10=1;MQ20=1;MQ30=1;MQ40=1;MQ50=1;SC=TGTATGTGTAAATATATATAT;set=variant2-variant3 GT:GQ:PS:UG:UQ...

Possible mis-assembly in mGorGor1 chr2_mat_hsa3:3,667,975-3,671,830

2

 A possible mis-assembly in the pCHT, with HiFi and ONT support. Read alignment indicates a ~1.6k region should be removed. Reported by Peter Kerpedijiev. View on [Resgen](https://resgen.io/paper-data/Yoo%202024%20-%20All/views/RDnlA-85RBOlohCB2CIcew)