Minor tweak to somatic whitelist

mskcc · Dec 9, 2016 · bebc30b · bebc30b
1 parent 4c7cf56
commit bebc30b
Showing 1 changed file with 6 additions and 8 deletions.
diff --git a/data/known_somatic_sites.bed b/data/known_somatic_sites.bed
@@ -3,10 +3,10 @@
 #
 # bcftools filter --targets-file ^known_somatic_sites.bed ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz
 #
-# This file aggregates known curated somatic variants from:
+# This file aggregates somatic variants from highly curated sources:
 # - Hotspots from Chang et al. minus some likely false positives (doi:10.1038/nbt.3391)
 # - Blood-related mutations (clonal hematopoietic expansion) from Xie et al. (doi:10.1038/nm.3733)
-# - Germline sites that are sometimes somatically mutated (MSH6:F1088, TP53:R290, TERT:E280, ASXL1:G645_G646, HNF1A:P291)
+# - Somatically mutable germline sites at MSH6:F1088, TP53:R290, TERT:E280, ASXL1:G645_G646
 #
 1	11169374	11169375	MTOR:I2500
 1	11169376	11169377	MTOR:I2500
@@ -183,7 +183,7 @@
 7	116412043	116412045	MET:SS116412044
 7	131241054	131241055	PODXL:S22
 7	136938368	136938369	PTN:K44
-7	140453131	140453136	BRAF:K601,BRAF:V600
+7	140453131	140453136	BRAF:V600,BRAF:K601
 7	140453144	140453145	BRAF:L597
 7	140453147	140453149	BRAF:G596
 7	140453153	140453155	BRAF:D594
@@ -208,7 +208,7 @@
 8	128750944	128750945	MYC:S161
 8	144733540	144733541	ZNF623:T500
 9	2837295	2837296	KIAA0020:K63
-9	5073769	5073770	JAK2:V617F
+9	5073769	5073770	JAK2:V617
 9	16436467	16436469	BNC2:S575
 9	21970968	21970970	CDKN2A:L130
 9	21971016	21971018	CDKN2A:P114
@@ -277,9 +277,6 @@
 12	112926887	112926889	PTPN11:G503
 12	112926907	112926910	PTPN11:Q510
 12	121176676	121176678	ACADS:R330
-12	121432114	121432115	HNF1A:P291fs
-12	121432117	121432118	HNF1A:P291fs
-12	121432123	121432124	HNF1A:P291
 12	133250288	133250289	POLE:V411
 12	133253183	133253185	POLE:P286
 13	20056685	20056686	TPTE2:M41
@@ -325,6 +322,7 @@
 17	4496466	4496467	SMTNL2:SS4496467
 17	6941598	6941599	SLC16A13:F158
 17	7576850	7576852	TP53:SS7576851
+17	7577060	7577062	TP53:R290fs
 17	7577068	7577070	TP53:R290,TP53:R290fs
 17	7577080	7577082	TP53:E286
 17	7577091	7577100	TP53:R280,TP53:D281,TP53:R282
@@ -424,7 +422,7 @@
 19	59010863	59010865	SLC27A5:T554
 20	20033085	20033087	CRNKL1:S128
 20	23028479	23028480	THBD:C554
-20	31022439	31022443	ASXL1:G645fs,ASXL1:G646fs
+20	31022438	31022442	ASXL1:G645fs,ASXL1:G646fs
 20	31022711	31022712	ASXL1:Q733
 20	34302143	34302145	RBM39:T353
 20	39832809	39832810	ZHX3:N249