From 2b6b6b062c5bd1197ae2fd96b770a77e287db94a Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Wed, 30 May 2018 17:54:54 +0200
Subject: [PATCH] Added normalization file for 50 kb based on HGSVC trio
 coverage. Enable 50kb in pipeline

---
 Snake.config.json                       |     5 +-
 Snakefile                               |     2 +-
 utils/normalization/norm.HGSVC.50kb.txt | 60608 ++++++++++++++++++++++
 3 files changed, 60613 insertions(+), 2 deletions(-)
 create mode 100644 utils/normalization/norm.HGSVC.50kb.txt

diff --git a/Snake.config.json b/Snake.config.json
index b6e541f..6c41edd 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -40,6 +40,9 @@
     "simulation_cell_count" : 100,
     "simulation_alpha" : 0.02,
 
-    "genome_size" : 3e9
+    "genome_size" : 3e9,
 
+    "normalization" : {
+        "50000_fixed" : "utils/normalization/norm.HGSVC.50kb.txt"
+    }
 }
diff --git a/Snakefile b/Snakefile
index b346af9..ef51fa3 100644
--- a/Snakefile
+++ b/Snakefile
@@ -26,7 +26,7 @@ rule all:
         expand("sv_calls/{sample}/{window}_fixed.{bpdens}/{method}.{chrom}.pdf",
                sample = SAMPLE,
                chrom = config["chromosomes"],
-               window = [100000],
+               window = [50000, 100000],
                bpdens = ["few","medium","more","many"],
                method = METHODS)
 
diff --git a/utils/normalization/norm.HGSVC.50kb.txt b/utils/normalization/norm.HGSVC.50kb.txt
new file mode 100644
index 0000000..35bfacc
--- /dev/null
+++ b/utils/normalization/norm.HGSVC.50kb.txt
@@ -0,0 +1,60608 @@
+chrom	start	end	BM150	cov	scalar	smooth2	mapp.frac	gc
+chr1	0	50000	0.0701147167439302	0.28278995877798	0.28278995877798	0.28278995877798	0.21654	0.48425
+chr1	50000	100000	0.0606294142810997	0.278960597936395	0.28278995877798	0.28278995877798	0.39234	0.37674
+chr1	100000	150000	0.175056716067952	0.349830635486328	0.28278995877798	0.28278995877798	0.53698	0.42996
+chr1	150000	200000	0.134481062009152	0.364325524296535	0.28278995877798	0.278960597936395	0.3209	0.48634
+chr1	200000	250000	0	0.0062445274721078	0.258136472527697	0.258136472527697	0.03442	0.48056352726324
+chr1	250000	300000	0.197698213147651	0.258136472527697	0.0062445274721078	0.0140376890624048	0.5511	0.391444593320431
+chr1	300000	350000	0	0	0.00333082329409007	0.0140376890624048	0	0.401574803149606
+chr1	350000	400000	0.00140449438202247	0.00333082329409007	0.00333082329409007	0.0140376890624048	0.05602	0.47474
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+chr1	127650000	127700000	0	0	0	0	0	NA
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+chr1	127750000	127800000	0	0	0	0	0	NA
+chr1	127800000	127850000	0	0	0	0	0	NA
+chr1	127850000	127900000	0	0	0	0	0	NA
+chr1	127900000	127950000	0	0	0	0	0	NA
+chr1	127950000	128000000	0	0	0	0	0	NA
+chr1	128000000	128050000	0	0	0	0	0	NA
+chr1	128050000	128100000	0	0	0	0	0	NA
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+chr1	128150000	128200000	0	0	0	0	0	NA
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+chr1	128250000	128300000	0	0	0	0	0	NA
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+chr1	128750000	128800000	0	0	0	0	0	NA
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+chr1	128850000	128900000	0	0	0	0	0	NA
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+chr1	129950000	130000000	0	0	0	0	0	NA
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+chr1	131050000	131100000	0	0	0	0	0	NA
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+chr1	131200000	131250000	0	0	0	0	0	NA
+chr1	131250000	131300000	0	0	0	0	0	NA
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+chr1	131350000	131400000	0	0	0	0	0	NA
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+chr1	131750000	131800000	0	0	0	0	0	NA
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+chr1	131850000	131900000	0	0	0	0	0	NA
+chr1	131900000	131950000	0	0	0	0	0	NA
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+chr1	132000000	132050000	0	0	0	0	0	NA
+chr1	132050000	132100000	0	0	0	0	0	NA
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+chr1	132150000	132200000	0	0	0	0	0	NA
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+chr1	132250000	132300000	0	0	0	0	0	NA
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+chr1	132650000	132700000	0	0	0	0	0	NA
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+chr1	132750000	132800000	0	0	0	0	0	NA
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+chr13	11450000	11500000	0	0	0	0	0	NA
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+chr13	11550000	11600000	0	0	0	0	0	NA
+chr13	11600000	11650000	0	0	0	0	0	NA
+chr13	11650000	11700000	0	0	0	0	0	NA
+chr13	11700000	11750000	0	0	0	0	0	NA
+chr13	11750000	11800000	0	0	0	0	0	NA
+chr13	11800000	11850000	0	0	0	0	0	NA
+chr13	11850000	11900000	0	0	0	0	0	NA
+chr13	11900000	11950000	0	0	0	0	0	NA
+chr13	11950000	12000000	0	0	0	0	0	NA
+chr13	12000000	12050000	0	0	0	0	0	NA
+chr13	12050000	12100000	0	0	0	0	0	NA
+chr13	12100000	12150000	0	0	0	0	0	NA
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+chr13	12300000	12350000	0	0	0	0	0	NA
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+chr13	12400000	12450000	0	0	0	0	0	NA
+chr13	12450000	12500000	0	0	0	0	0	NA
+chr13	12500000	12550000	0	0	0	0	0	NA
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+chr13	12650000	12700000	0	0	0	0	0	NA
+chr13	12700000	12750000	0	0	0	0	0	NA
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+chr13	15950000	16000000	0	8.83236177353824e-05	8.83236177353824e-05	8.83236177353824e-05	0	NA
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+chr14	8700000	8750000	0	0	0	0	0	NA
+chr14	8750000	8800000	0	0	0	0	0	NA
+chr14	8800000	8850000	0	0	0	0	0	NA
+chr14	8850000	8900000	0	0	0	0	0	NA
+chr14	8900000	8950000	0	0	0	0	0	NA
+chr14	8950000	9000000	0	0	0	0	0	NA
+chr14	9000000	9050000	0	0	0	0	0	NA
+chr14	9050000	9100000	0	0	0	0	0	NA
+chr14	9100000	9150000	0	0	0	0	0	NA
+chr14	9150000	9200000	0	0	0	0	0	NA
+chr14	9200000	9250000	0	0	0	0	0	NA
+chr14	9250000	9300000	0	0	0	0	0	NA
+chr14	9300000	9350000	0	0	0	0	0	NA
+chr14	9350000	9400000	0	0	0	0	0	NA
+chr14	9400000	9450000	0	0	0	0	0	NA
+chr14	9450000	9500000	0	0	0	0	0	NA
+chr14	9500000	9550000	0	0	0	0	0	NA
+chr14	9550000	9600000	0	0	0	0	0	NA
+chr14	9600000	9650000	0	0	0	0	0	NA
+chr14	9650000	9700000	0	0	0	0	0	NA
+chr14	9700000	9750000	0	0	0	0	0	NA
+chr14	9750000	9800000	0	0	0	0	0	NA
+chr14	9800000	9850000	0	0	0	0	0	NA
+chr14	9850000	9900000	0	0	0	0	0	NA
+chr14	9900000	9950000	0	0	0	0	0	NA
+chr14	9950000	10000000	0	0	0	0	0	NA
+chr14	10000000	10050000	0	0	0	0	0	NA
+chr14	10050000	10100000	0	0	0	0	0	NA
+chr14	10100000	10150000	0	0	0	0	0	NA
+chr14	10150000	10200000	0	0	0	0	0	NA
+chr14	10200000	10250000	0	0	0	0	0	NA
+chr14	10250000	10300000	0	0	0	0	0	NA
+chr14	10300000	10350000	0	0	0	0	0	NA
+chr14	10350000	10400000	0	0	0	0	0	NA
+chr14	10400000	10450000	0	0	0	0	0	NA
+chr14	10450000	10500000	0	0	0	0	0	NA
+chr14	10500000	10550000	0	0	0	0	0	NA
+chr14	10550000	10600000	0	0	0	0	0	NA
+chr14	10600000	10650000	0	0	0	0	0	NA
+chr14	10650000	10700000	0	0	0	0	0	NA
+chr14	10700000	10750000	0	0	0	0	0	NA
+chr14	10750000	10800000	0	0	0	0	0	NA
+chr14	10800000	10850000	0	0	0	0	0	NA
+chr14	10850000	10900000	0	0	0	0	0	NA
+chr14	10900000	10950000	0	0	0	0	0	NA
+chr14	10950000	11000000	0	0	0	0	0	NA
+chr14	11000000	11050000	0	0	0	0	0	NA
+chr14	11050000	11100000	0	0	0	0	0	NA
+chr14	11100000	11150000	0	0	0	0	0	NA
+chr14	11150000	11200000	0	0	0	0	0	NA
+chr14	11200000	11250000	0	0	0	0	0	NA
+chr14	11250000	11300000	0	0	0	0	0	NA
+chr14	11300000	11350000	0	0	0	0	0	NA
+chr14	11350000	11400000	0	0	0	0	0	NA
+chr14	11400000	11450000	0	0	0	0	0	NA
+chr14	11450000	11500000	0	0	0	0	0	NA
+chr14	11500000	11550000	0	0	0	0	0	NA
+chr14	11550000	11600000	0	0	0	0	0	NA
+chr14	11600000	11650000	0	0	0	0	0	NA
+chr14	11650000	11700000	0	0	0	0	0	NA
+chr14	11700000	11750000	0	0	0	0	0	NA
+chr14	11750000	11800000	0	0	0	0	0	NA
+chr14	11800000	11850000	0	0	0	0	0	NA
+chr14	11850000	11900000	0	0	0	0	0	NA
+chr14	11900000	11950000	0	0	0	0	0	NA
+chr14	11950000	12000000	0	0	0	0	0	NA
+chr14	12000000	12050000	0	0	0	0	0	NA
+chr14	12050000	12100000	0	0	0	0	0	NA
+chr14	12100000	12150000	0	0	0	0	0	NA
+chr14	12150000	12200000	0	0	0	0	0	NA
+chr14	12200000	12250000	0	0	0	0	0	NA
+chr14	12250000	12300000	0	0	0	0	0	NA
+chr14	12300000	12350000	0	0	0	0	0	NA
+chr14	12350000	12400000	0	0	0	0	0	NA
+chr14	12400000	12450000	0	0	0	0	0	NA
+chr14	12450000	12500000	0	0	0	0	0	NA
+chr14	12500000	12550000	0	0	0	0	0	NA
+chr14	12550000	12600000	0	0	0	0	0	NA
+chr14	12600000	12650000	0	0	0	0	0	NA
+chr14	12650000	12700000	0	0	0	0	0	NA
+chr14	12700000	12750000	0	0	0	0	0	NA
+chr14	12750000	12800000	0	0	0	0	0	NA
+chr14	12800000	12850000	0	0	0	0	0	NA
+chr14	12850000	12900000	0	0	0	0	0	NA
+chr14	12900000	12950000	0	0	0	0	0	NA
+chr14	12950000	13000000	0	0	0	0	0	NA
+chr14	13000000	13050000	0	0	0	0	0	NA
+chr14	13050000	13100000	0	0	0	0	0	NA
+chr14	13100000	13150000	0	0	0	0	0	NA
+chr14	13150000	13200000	0	0	0	0	0	NA
+chr14	13200000	13250000	0	0	0	0	0	NA
+chr14	13250000	13300000	0	0	0	0	0	NA
+chr14	13300000	13350000	0	0	0	0	0	NA
+chr14	13350000	13400000	0	0	0	0	0	NA
+chr14	13400000	13450000	0	0	0	0	0	NA
+chr14	13450000	13500000	0	0	0	0	0	NA
+chr14	13500000	13550000	0	0	0	0	0	NA
+chr14	13550000	13600000	0	0	0	0	0	NA
+chr14	13600000	13650000	0	0	0	0	0	NA
+chr14	13650000	13700000	0	0	0	0	0	NA
+chr14	13700000	13750000	0	0	0	0	0	NA
+chr14	13750000	13800000	0	0	0	0	0	NA
+chr14	13800000	13850000	0	0	0	0	0	NA
+chr14	13850000	13900000	0	0	0	0	0	NA
+chr14	13900000	13950000	0	0	0	0	0	NA
+chr14	13950000	14000000	0	0	0	0	0	NA
+chr14	14000000	14050000	0	0	0	0	0	NA
+chr14	14050000	14100000	0	0	0	0	0	NA
+chr14	14100000	14150000	0	0	0	0	0	NA
+chr14	14150000	14200000	0	0	0	0	0	NA
+chr14	14200000	14250000	0	0	0	0	0	NA
+chr14	14250000	14300000	0	0	0	0	0	NA
+chr14	14300000	14350000	0	0	0	0	0	NA
+chr14	14350000	14400000	0	0	0	0	0	NA
+chr14	14400000	14450000	0	0	0	0	0	NA
+chr14	14450000	14500000	0	0	0	0	0	NA
+chr14	14500000	14550000	0	0	0	0	0	NA
+chr14	14550000	14600000	0	0	0	0	0	NA
+chr14	14600000	14650000	0	0	0	0	0	NA
+chr14	14650000	14700000	0	0	0	0	0	NA
+chr14	14700000	14750000	0	0	0	0	0	NA
+chr14	14750000	14800000	0	0	0	0	0	NA
+chr14	14800000	14850000	0	0	0	0	0	NA
+chr14	14850000	14900000	0	0	0	0	0	NA
+chr14	14900000	14950000	0	0	0	0	0	NA
+chr14	14950000	15000000	0	0	0	0	0	NA
+chr14	15000000	15050000	0	0	0	0	0	NA
+chr14	15050000	15100000	0	0	0	0	0	NA
+chr14	15100000	15150000	0	0	0	0	0	NA
+chr14	15150000	15200000	0	0	0	0	0	NA
+chr14	15200000	15250000	0	0	0	0	0	NA
+chr14	15250000	15300000	0	0	0	0	0	NA
+chr14	15300000	15350000	0	0	0	0	0	NA
+chr14	15350000	15400000	0	0	0	0	0	NA
+chr14	15400000	15450000	0	0	0	0	0	NA
+chr14	15450000	15500000	0	0	0	0	0	NA
+chr14	15500000	15550000	0	0	0	0	0	NA
+chr14	15550000	15600000	0	0	0	0	0	NA
+chr14	15600000	15650000	0	0	0	0	0	NA
+chr14	15650000	15700000	0	0	0	0	0	NA
+chr14	15700000	15750000	0	0	0	0	0	NA
+chr14	15750000	15800000	0	0	0	0	0	NA
+chr14	15800000	15850000	0	0	0	0	0	NA
+chr14	15850000	15900000	0	0	0	0	0	NA
+chr14	15900000	15950000	0	0	0	0	0	NA
+chr14	15950000	16000000	0	0	0	0	0	NA
+chr14	16000000	16050000	0.0949921489247332	0.138808319861554	0.138808319861554	0	0.30324	0.475751927785696
+chr14	16050000	16100000	0.706997839863008	0.919322335310032	0.138808319861554	0	0.5107	0.383437310458366
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+chr14	16200000	16250000	0	0	0	0	0	NA
+chr14	16250000	16300000	0	0	0	0	0	NA
+chr14	16300000	16350000	0	0	0	0	0	NA
+chr14	16350000	16400000	0	0	0	0	0	NA
+chr14	16400000	16450000	0.195955230786691	0.125466801592035	0	0	0.07808	0.377299880525687
+chr14	16450000	16500000	0	0	0	0	0	NA
+chr14	16500000	16550000	0	0	0	0	0	NA
+chr14	16550000	16600000	0	0	0	0	0	NA
+chr14	16600000	16650000	0	0	0	0	0	NA
+chr14	16650000	16700000	0	0	0	0	0	NA
+chr14	16700000	16750000	0	0	0	0	0	NA
+chr14	16750000	16800000	0	0	0	0	0	NA
+chr14	16800000	16850000	0	0	0	0	0	NA
+chr14	16850000	16900000	0	0	0	0	0	NA
+chr14	16900000	16950000	0	0	0	0	0	NA
+chr14	16950000	17000000	0	0	0	0	0	NA
+chr14	17000000	17050000	0	0	0	0	0	NA
+chr14	17050000	17100000	0	0	0	0	0	NA
+chr14	17100000	17150000	0	0	0	0	0	NA
+chr14	17150000	17200000	0	0	0	0	0	NA
+chr14	17200000	17250000	0	0	0	0	0	NA
+chr14	17250000	17300000	0	0	0	0	0	NA
+chr14	17300000	17350000	0	0	0	0	0	NA
+chr14	17350000	17400000	0	0	0	0	0	NA
+chr14	17400000	17450000	0	0	0	0	0	NA
+chr14	17450000	17500000	0	0	0	0	0	NA
+chr14	17500000	17550000	0	0	0	0	0	NA
+chr14	17550000	17600000	0	0	0	0	0	NA
+chr14	17600000	17650000	0	0	0	0	0	NA
+chr14	17650000	17700000	0	0	0	0	0	NA
+chr14	17700000	17750000	0	0	0	0	0	NA
+chr14	17750000	17800000	0	0	0	0	0	NA
+chr14	17800000	17850000	0	0	0	0	0	NA
+chr14	17850000	17900000	0	0	0	0	0	NA
+chr14	17900000	17950000	0	0	0	0	0	NA
+chr14	17950000	18000000	0	0	0	0	0	NA
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+chr14	18200000	18250000	0.412695762414864	0.354839341177948	0.354839341177948	0.232775133814528	0.45038	0.370774634588511
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+chr14	18750000	18800000	0	0	0	0.308217517104907	0	NA
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+chr14	18850000	18900000	0.288210728098369	0.186635101001857	0.186635101001857	0.308217517104907	0.55656	0.424429810472213
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+chr20	18100000	18150000	0.99619618833102	0.883195066747175	1.13387444499041	1.13387444499041	0.99124	0.41174
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+chr20	18250000	18300000	1.12782532698263	1.20527123641891	1.1125425151494	1.1125425151494	0.99924	0.41824
+chr20	18300000	18350000	0.914597294091676	0.909367152827082	1.1125425151494	1.1125425151494	1	0.38274
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+chr20	18400000	18450000	1.08962663428956	1.09088393433696	1.09088393433696	1.1125425151494	1	0.40946
+chr20	18450000	18500000	1.11173289881155	1.08719583474628	1.09088393433696	1.18293572953213	0.99672	0.41096
+chr20	18500000	18550000	1.02027167588965	1.18293572953213	1.09088393433696	1.18293572953213	1	0.4356
+chr20	18550000	18600000	1.01167973724153	1.02036488617889	1.18293572953213	1.19655775308903	0.9998	0.42684
+chr20	18600000	18650000	1.07049878959991	1.19655775308903	1.19655775308903	1.19655775308903	0.99244	0.42728
+chr20	18650000	18700000	1.17004103886126	1.26545713916625	1.26545713916625	1.19655775308903	1	0.4305
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+chr20	18800000	18850000	1.36928670580356	1.6448838785634	1.42941669596974	1.42941669596974	0.9993	0.44468
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+chr20	18900000	18950000	1.30962402142177	1.42941669596974	1.42941669596974	1.4403737095371	0.9999	0.41738
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-- 
GitLab