Recommended FT filter parameters

[zhujiahua700403]

Thank you for developing the software. I note that graphtyper2 has a series of parameters for genotyping population structural variation. I would like to know what filtering conditions are recommended. For instance, should genotypes with FT values of FAIL1-3 be marked as ./.? In a previous paper, a proposal was put forward: “（ SVTYPE = DEL &; QD > 12 &; （ ABHet > 0.30 |ABHet < 0 ） &; （ AC / NUM_MERGED_SVS ） < 25 ） |（ SVTYPE = DUP & QD > 5 &; （ AC / NUM_MERGED_SVS ） < 25 ） |（ SVTYPE = INS &; （ AC / NUM_MERGED_SVS ） < 25 &; （ ABHet > 0.25 |ABHet < 0 ） &; MaxAAS > 4 ） |（ SVTYPE = INV &; （ AC / NUM_MERGED_SVS ） < 25 &; （ ABHet > 0.25 |ABHet < 0 ） &; MaxAAS > 4 ）. And SV genotypes with depth (DP) < 1 or genotype quality (GQ) < 13 shall be set as missing genotypes. If the NGS data have read coverage larger than 10, users can skip steps “b” and “c” and modify the command in our pipeline to the following command: “( SVTYPE = DEL & QD > 12 & ( ABHet > 0.30 | ABHet < 0 ) & ( AC / NUM_MERGED_SVS ) < 25 & PASS_AC > 0 & PASS_ratio > 0.1 ) | ( SVTYPE = DUP & QD > 5 & PASS_AC > 0 & ( AC / NUM_MERGED_SVS ) < 25 ) | ( SVTYPE = INS & PASS_AC > 0 & ( AC / NUM_MERGED_SVS ) < 25 & PASS_ratio > 0.1 & ( ABHet > 0.25 | ABHet < 0 ) & MaxAAS > 4 ) | ( SVTYPE = INV & PASS_AC > 0 & ( AC / NUM_MERGED_SVS ) < 25 & PASS_ratio > 0.1 & ( ABHet > 0.25 | ABHet < 0 ) & MaxAAS > 4 )”. However, I would like to know the recommended filtering method for GQ values exceeding 10X. I hope you could offer me some advice.