18 November 2021
Jeffrey M. Kidd
University of Michigan


This directory contains structural variant for 1,987 samples processed by the Dog10K
Consortium.

Calls were identified in each sample using Manta version 1.6.0 with default parameters.
Inversion were converted to event representation using the convertInversion.py utility. 
Raw calls were merged using svimmer and genotyped across all samples using GraphTyper2 
version 2.7.2 with default parameters. All analyiss was limited to the primary
assembled chromosomes.

For break-end (BND), insertion (INS), deletion (DEL) and duplication (DUP) calls, the 
‘AGGREGATED’ genotyping model was used.  For inversion (INV) candidates, the breakpoint 
model was used as reported by GraphTyper2. 

Variants were filtered using vcffilter with the following command: 

vcffilter -f "( SVTYPE = BND & SVMODEL = AGGREGATED & QD > 20 & ( ABHet > 0.30 | ABHet < 0 ) & ( AC / NUM_MERGED_SVS ) < 10 & PASS_AC > 0 & PASS_ratio > 0.1 ) | ( SVTYPE = DEL & SVMODEL = AGGREGATED & QD > 12 & ( ABHet > 0.30 | ABHet < 0 ) & ( AC / NUM_MERGED_SVS ) < 25 & PASS_AC > 0 & PASS_ratio > 0.1 ) | ( SVTYPE = DUP & SVMODEL = AGGREGATED & QD > 5 & PASS_AC > 0 & ( AC / NUM_MERGED_SVS ) < 25 ) | ( SVTYPE = INS & SVMODEL = AGGREGATED & 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 )" 



Variant Type	Raw Merged Calls	Pass GraphTyper2 Filters
BND	            2,270,095 	        189
DEL	            166,416 	        75,337
DUP	            29,819 	            3,453
INS	            220,651 	        66,328
INV	            10,372 	            1,806
Total	        2,697,353 	        147,113