From 7852856b15a234ba7b8b22ae4872d8edc7420e08 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Tue, 18 Sep 2018 15:05:52 +0200
Subject: [PATCH] MPII paths for now
---
Snake.config.json | 17 ++++++-----------
1 file changed, 6 insertions(+), 11 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 9b6890d..89ed2b4 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -1,21 +1,16 @@
{
"chromosomes" : ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX"],
- "reference" : "/g/korbel/shared/datasets/refgenomes/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
- "mosaicatcher" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/build/mosaicatcher",
- "plot_script" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/qc.R",
- "sv_plot_script": "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/chrom.R",
- "norm_script" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher_experimental/R/norm.R",
+ "reference" : "/MMCI/TM/scratch/ref/GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
+ "mosaicatcher" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/build/mosaic",
+ "plot_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/qc.R",
+ "norm_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/norm.R",
"samtools" : "samtools",
"bcftools" : "bcftools",
- "snv_calls" : {
- "C7_data" : "/g/korbel2/StrandSeq/20180221_RPE_Data/regenSNVs_GRCh38sites_C7_chr1-22plusX.filtered.vcf.gz",
- "RPE-BM510" : "/g/korbel2/StrandSeq/20180221_RPE_Data/regenSNVs_GRCh38sites_BM510_chr1-22plusX.filtered.vcf.gz",
- "RPE1-WT" : "/g/korbel2/StrandSeq/20180606_RPE1-WT/regenSNVs_GRCh38sites_RPEWTstrandS_chr1-22plusX.filtered.vcf.gz"
- },
+ "snv_sites_to_genotype": "/MMCI/TM/scratch/MosaiCatcher_data/RPE1_cell_lines/Compare_SNVsCalls/GRCh38_1000G_variableSites/ALL.chr1-22plusX_GRCh38_sites.20170504.renamedCHR.vcf.gz",
- "snv_sites_to_genotype": "",
+ "snv_calls" : {},
"variable_bins" : {
"50000" : "utils/variable_bins.GRCh38.50kb.bed",
--
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