diff --git a/cnv/cnvkit_germline_blacklist_20240613.bed b/cnv/cnvkit_germline_blacklist_20240613.bed new file mode 100644 index 0000000..1fe3062 --- /dev/null +++ b/cnv/cnvkit_germline_blacklist_20240613.bed @@ -0,0 +1,20 @@ +chr1 1016500 1019000 Clorf159(UTR) +chr1 120611500 120612500 FANCD2 +chr1 161436450 161436550 intergenic +chr2 113984200 113984300 PAX8(intron) +chr2 113993500 133994000 PAX8-AS1 +chr3 10088000 10090000 FANCD2 +chr3 75741000 75741500 intergenic +chr6 29910000 29914000 HLA-A +chr6 31236000 31240000 HLA-C +chr6 31321000 31326000 HLA-B +chr7 55234000 55235500 EGFR(intron) +chr7 57612500 57612700 intergenic +chr7 142458000 142461000 PRSS1(UTR) +chr7 151920000 151980000 KMTC2 +chr9 68427500 68428000 FRL1JP +chr11 1015000 1019000 MUC6 +chr17 16060000 16100000 NCOR1 +chr17 45190000 45270000 CDC27 +chr20 29633500 29634500 FRG1B(UTR) +chr22 42522000 42529000 CYP2D6 diff --git a/cnv/cnvkit_germline_blacklist_20240613_hg38.bed b/cnv/cnvkit_germline_blacklist_20240613_hg38.bed new file mode 100644 index 0000000..d386d30 --- /dev/null +++ b/cnv/cnvkit_germline_blacklist_20240613_hg38.bed @@ -0,0 +1,20 @@ +chr1 1081120 1083620 Clorf159(UTR) +chr1 120068886 120069886 FANCD2 +chr1 161466660 161466760 intergenic +chr2 113226623 113226723 PAX8(intron) +chr2 113235923 133236428 PAX8-AS1 +chr3 10046316 10048316 FANCD2 +chr3 75691849 75692349 intergenic +chr6 29942223 29946223 HLA-A +chr6 31268223 31272223 HLA-C +chr6 31353223 31358223 HLA-B +chr7 55166307 55167807 EGFR(intron) +chr7 57552794 57552994 intergenic +chr7 142750149 142753149 PRSS1(UTR) +chr7 152222915 152282915 KMTC2 +chr9 63831766 63832266 FRL1JP +chr11 1015000 1019000 MUC6 +chr17 16156686 16196686 NCOR1 +chr17 47112634 47192634 CDC27 +chr20 30398824 30399824 FRG1B(UTR) +chr22 42125995 42132993 CYP2D6