added iNATT study and version bump

mcgml · Jan 30, 2018 · a495b66 · a495b66
1 parent 6aad3c3
commit a495b66
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Showing 4 changed files with 35 additions and 1 deletion.
diff --git a/1_SomaticAmplicon.sh b/1_SomaticAmplicon.sh
@@ -8,7 +8,7 @@ cd $PBS_O_WORKDIR
 #Description: Somatic Amplicon Pipeline (Illumina paired-end). Not for use with other library preps/ experimental conditions.
 #Author: Matt Lyon, All Wales Medical Genetics Lab
 #Mode: BY_SAMPLE
-version="1.7.3"
+version="1.7.4"
 
 # Directory structure required for pipeline
 #

diff --git a/NGHS-101X/hotspot_coverage/AKT1.bed b/NGHS-101X/hotspot_coverage/AKT1.bed
@@ -0,0 +1 @@
+14	105246469	105246573	AKT1 e4
diff --git a/NGHS-101X/hotspot_coverage/RET.bed b/NGHS-101X/hotspot_coverage/RET.bed
@@ -0,0 +1,5 @@
+10	43609064	43609143	RET e10
+10	43609907	43609978	RET e11
+10	43613800	43613929	RET e13
+10	43615536	43615671	RET e15
+10	43617373	43617484	RET e16
diff --git a/NGHS-101X/hotspot_variants/iNATT.bed b/NGHS-101X/hotspot_variants/iNATT.bed
@@ -0,0 +1,28 @@
+1	115252201	115252204	NRAS c146
+1	115252288	115252291	NRAS c117
+1	115256527	115256529	NRAS c61
+1	115258742	115258748	NRAS c12_13
+3	178936081	178936096	PIK3CA c542_546
+3	178952083	178952092	PIK3CA c1047_1049
+7	140453131	140453140	BRAF c599_601
+10	43609064	43609143	RET e10
+10	43609907	43609978	RET e11
+10	43613800	43613929	RET e13
+10	43615536	43615671	RET e15
+10	43617373	43617484	RET e16
+12	25378559	25378562	KRAS c146
+12	25378646	25378649	KRAS c117
+12	25380274	25380277	KRAS c61
+12	25398279	25398285	KRAS c12_13
+14	105246469	105246573	AKT1 e4
+17	7572921	7573013	TP53 e12
+17	7573921	7574038	TP53 e11
+17	7576519	7576662	TP53 e10
+17	7576847	7576931	TP53 e9
+17	7577013	7577160	TP53 e8
+17	7577493	7577613	TP53 e7
+17	7578171	7578294	TP53 e6
+17	7578365	7578559	TP53 e5
+17	7579306	7579595	TP53 e4
+17	7579694	7579726	TP53 e3
+17	7579833	7579945	TP53 e2