From 88b7760871a3fedec6ecbd044d519bded2e04413 Mon Sep 17 00:00:00 2001 From: Mathieu Quinodoz <46816306+mquinodo@users.noreply.github.com> Date: Tue, 25 Aug 2020 11:11:46 +0200 Subject: [PATCH] Update AutoMap_v1.0.sh --- AutoMap_v1.0.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AutoMap_v1.0.sh b/AutoMap_v1.0.sh index ded3825..152ce36 100644 --- a/AutoMap_v1.0.sh +++ b/AutoMap_v1.0.sh @@ -3,7 +3,7 @@ usage() { echo "## ERROR: Usage: $0 [--vcf <string>] [--genome <hg19|hg38>] [--out <string>] [--common] [--id <string>] [--panel <string>] [--panelname <string>] [--DP <0-99>] [--binomial <0-1.0>] [--percaltlow <0-1.0>] [--percalthigh <0-1.0>] [--window <3-999>] [--windowthres <1-999>] [--minsize <0-99>] [--minvar <1-999>] [--minperc <0-100>] [--maxgap <0-1000Mb>] [--chrX] [--extend <0-100Mb>]. Exit." 1>&2; exit 1; } numbervar() { echo "## ERROR: Less than 10,000 variants ($nbvar detected variants) with AD and DP available. Exit." 1>&2; exit 1; } numbervar2() { echo "## ERROR: Less than 10,000 variants with good quality detected (only $nbvar passing QC). Exit." 1>&2; exit 1; } -multivcf() { echo "## ERROR: Mutli-sample VCF file, please run AutoMap with --multi option. Exit." 1>&2; exit 1; } +multivcf() { echo "## ERROR: Multi-sample VCF file, please run AutoMap with --multivcf option. Exit." 1>&2; exit 1; } multivcf2() { echo "## ERROR: Please analyze only one mutli-sample VCF file at a time. Exit." 1>&2; exit 1; } multivcf3() { echo "## ERROR: Please do not use --id or --common option with mutli-sample VCF file. Exit." 1>&2; exit 1; } nobcftools() { echo "## ERROR: bcftools lower than v1.9 -> Please Update! Exit." 1>&2; exit 1; }