From f7fa6c66eb9d6ed28e1bfba49ca0b272b2b18211 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 11 Jan 2018 14:02:35 +0100
Subject: [PATCH] Require external VCF to be zipped and indexed
---
README.md | 21 +++++++++++++++++----
Snakefile | 3 ++-
2 files changed, 19 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index 3c82929..8af551f 100644
--- a/README.md
+++ b/README.md
@@ -15,17 +15,17 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
source("https://bioconductor.org/biocLite.R")
biocLite('BSgenome.Hsapiens.UCSC.hg38')
```
- * [Strand-Phaser](https://github.com/daewoooo/StrandPhaseR) is installed automagically
+ * [Strand-Phaser](https://github.com/daewoooo/StrandPhaseR) is installed automatically
2. **Set up the configuration of the smakemake pipeline**
* Open `Snake.config.json` and specify the path to the executatables
(such as Mosaicatcher) and to the R scripts.
* Create a subdirectory `bam/` and another subdirectory per sample (e.g.
- `bam/NA12878`). **Multiple samples can be run together not**.
+ `bam/NA12878/`). **Multiple samples can be run together not**.
Then copy (or soft-link) the Strand-seq single-cell libraries (one BAM
- file per cell) in there. Note that bam files need to contain a read group
- and should have duplicates marked.
+ file per cell) in there. Note that bam files need to be sorted and indexed,
+ contain a read group and should have duplicates marked.
3. **Run Snakemake**
@@ -37,3 +37,16 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
--cluster-config Snake.cluster.json \
--cluster "???"
```
+
+### SNV calls
+
+ The pipeline will run simple SNV calling using [samtools](https://github.com/samtools/samtools)
+ and [bcftools](https://github.com/samtools/bcftools). If you **already have
+ SNV calls**, you can avoid that by entering your VCF files into the pipeline.
+ To so, make sure the files are [tabix](https://github.com/samtools/tabix)-indexed
+ and specifigy them inside the `Snake.config.json` file:
+ ```
+ "snv_calls" : {
+ "NA12878" : "path/to/snp/calls.vcf.gz"
+ },
+ ```
diff --git a/Snakefile b/Snakefile
index 1d58145..12a4480 100644
--- a/Snakefile
+++ b/Snakefile
@@ -422,7 +422,8 @@ rule merge_SNV_calls:
rule split_external_snv_calls:
input:
- vcf = lambda wc: config["snv_calls"][wc.sample]
+ vcf = lambda wc: config["snv_calls"][wc.sample],
+ tbi = lambda wc: config["snv_calls"][wc.sample] + ".tbi"
output:
vcf = "external_snv_calls/{sample}/{chrom}.vcf"
log: "log/{sample}/external_snv_calls.{chrom}.vcf.log"
--
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