Merge pull request #42 from genomic-medicine-sweden/cnv_plot_rm_MUC6

feat: rm noisy MUC6 from cnv VAF plot
genomic-medicine-sweden · Jun 14, 2024 · dc476e6 · dc476e6
2 parents 7225811 + 4a36fdf
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diff --git a/cnv/cnvkit_germline_blacklist_20240613.bed 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
@@ -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