From 2d8f8287f57add4e9e94d16ff8c5041beadabece Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 24 Sep 2018 16:36:13 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: add cmd for Mutect2

---
 src/1_JU28_59vs17_SNP_calling.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index 19c2d0e..ed4e9f0 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -1,3 +1,6 @@
 #!/bin/sh
 ./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" -resume -w ~/data/work/
 
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/
+
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/ --tumor "NG-10944_JU2859_bis_lib169352_5217_1" --normal "MR_550_clean"
-- 
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