From d580c130c863c802adb20dce4c6b3930dfc2c8f8 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Wed, 10 Jan 2018 18:19:54 +0100
Subject: [PATCH] Add config option snv_calls to use existing SNV call sets
---
Snake.config.json | 1 +
Snakefile | 21 ++++++++++++++++++---
2 files changed, 19 insertions(+), 3 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 53cd157..eb71bc7 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -10,6 +10,7 @@
"samtools" : "samtools",
"bcftools" : "bcftools",
+ "snv_calls" : "",
"exclude_file" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/data/exclude/hg19.exclude",
"variable_bins" : {
diff --git a/Snakefile b/Snakefile
index 4b8811b..9c82b17 100644
--- a/Snakefile
+++ b/Snakefile
@@ -289,13 +289,16 @@ rule prepare_strandphaser_config_per_chrom:
print("bsGenome = '", config["R_reference"], "'", sep = "", file = f)
-
+def locate_snv_vcf(wildcards):
+ if config["snv_calls"] == "":
+ return "snv_calls/{}.{}.vcf".format(config["sample"], wildcards.chrom)
+ else:
+ return "external_snv_calls/{}.{}.vcf".format(config["sample"], wildcards.chrom)
rule run_strandphaser_per_chrom:
input:
- mergedbam = "snv_calls/merged.bam",
wcregions = "strand_states/" + config["sample"] + ".strandphaser_input.txt",
- snppositions = "snv_calls/" + config["sample"] + ".{chrom}.vcf",
+ snppositions = locate_snv_vcf,
configfile = "log/StrandPhaseR.{chrom}.config",
strandphaser = "utils/R-packages/StrandPhaseR/R/StrandPhaseR",
bamfolder = "bam"
@@ -402,3 +405,15 @@ rule merge_SNV_calls:
shell:
config["bcftools"] + " concat -O v -o {output} {input}"
+rule split_external_snv_calls:
+ input:
+ vcf = config["snv_calls"]
+ output:
+ vcf = "external_snv_calls/" + config["sample"] + ".{chrom}.vcf"
+ log: "external_snv_calls/" + config["sample"] + ".{chrom}.vcf.log"
+ params:
+ bcftools = config["bcftools"],
+ #sample = config["sample"]
+ shell:
+ "({params.bcftools} view --samples " + config["sample"] + " --types snps {input.vcf} {wildcards.chrom} | bcftools view --genotype het - > {output.vcf}) > {log} 2>&1"
+
--
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