From a678f0e9fcfaf17d4ea33cf791b915c3c6a25105 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Sun, 28 Oct 2018 11:12:30 +0100
Subject: [PATCH] Important flag *sn_sites_to_genotype* in the configfile. This
overwrites the entry from *Snake.config.json*. The file it points to has to
be provided by the user (too big to include into image)
---
Snake.config-singularity.json | 7 +------
1 file changed, 1 insertion(+), 6 deletions(-)
diff --git a/Snake.config-singularity.json b/Snake.config-singularity.json
index 464c7bf..5342876 100644
--- a/Snake.config-singularity.json
+++ b/Snake.config-singularity.json
@@ -1,6 +1,7 @@
{
"chromosomes" : ["chrX","chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX"],
+ "snv_sites_to_genotype" : "snv_sites_to_genotype/ALL.chr1-22plusX_GRCh38_sites.20170504.renamedCHR.vcf.gz",
"reference" : "/reference.fa",
"mosaicatcher" : "mosaic",
@@ -10,12 +11,6 @@
"samtools" : "samtools",
"bcftools" : "bcftools",
- "snv_calls" : {
- "C7_data" : "external_info/regenSNVs_GRCh38sites_C7_chr1-22plusX.filtered.vcf.gz",
- "RPE-BM510" : "external_info/regenSNVs_GRCh38sites_BM510_chr1-22plusX.filtered.vcf.gz",
- "RPE1-WT" : "external_info/regenSNVs_GRCh38sites_RPEWTstrandS_chr1-22plusX.filtered.vcf.gz"
- },
-
"variable_bins" : {
"50000" : "utils/variable_bins.GRCh38.50kb.bed",
"100000" : "utils/variable_bins.GRCh38.100kb.bed"
--
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