The variants found in non-autism subject were excluded.

The genomic coordinates were converted from GRCh38/hg38 to GRCh37/hg19 human genome assembly using LiftOver.

The following genomic coordinates could not be mapped:

chr1:223554627-223554627
chr10:126941694-126941694
chr10:126947954-126947954
chr10:46389873-46389873
chr11:71060138-71060138
chr11:71060845-71060845
chr11:71064579-71064579
chr11:71066039-71066039
chr11:71066151-71066151
chr11:71067181-71067181
chr11:71069684-71069684
chr11:71077997-71077997
chr12:122093939-122093939
chr14:106349365-106349365
chr14:106349531-106349531
chr14:479809-479809
chr17:146951-146951
chr17:149059-149059
chr17:74893533-74893533
chr17:74893533-74893533
chr17:74893533-74893533
chr2:148933585-148933585
chr2:233140553-233140553
chr2:238894901-238894901
chr2:238896362-238896362
chr2:238905974-238905974
chr2:238909987-238909987
chr2:88861560-88861560
chr20:36309373-36309373
chr21:41830589-41830589
chr3:57381219-57381219
chr3:57385088-57385088
chr3:66184602-66184602
chr3:66184638-66184638
chr3:66197539-66197539
chr3:66218963-66218963
chr6:57507569-57507569
chr6:57523092-57523092
chr6:57527381-57527381
chr6:57529340-57529340
chr6:57568885-57568885
chr7:130526518-130526518
chr7:130526537-130526537
chr7:130534046-130534046
chr7:130548376-130548376
chr7:130549873-130549873
chr7:130550439-130550439
chr7:139700347-139700347
chr7:240328-240328
chr8:144021296-144021296
chr8:144026994-144026994
chr8:144029316-144029316
chr8:2083446-2083446
chr8:2083446-2083446
chr9:133383227-133383227
chrX:152766728-152766728

And the cooresponding variants were excluded.

There were 645 variants for which the reference base was wrong, but not necessarily because the gene was on the negative strand, so it was difficult to systematically fix these. All these variants were excluded.