diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh index 7ae4b162729d22884cc3e39d71adaca20907cb1d..f52e5057a4547f34d332bfd2595ebf3078b285d4 100755 --- a/variants/cnvkit.sh +++ b/variants/cnvkit.sh @@ -43,26 +43,12 @@ then fi if [[ -z $normals ]] || [[ -z $targets ]] then - if [[ $capture == "${index_path}/UTSWV2.bed" ]] - then - normals="${index_path}/UTSWV2.normals.cnn" - targets="${index_path}/UTSWV2.cnvkit_" - if [[ $umi == 'umi' ]] - then - normals="${index_path}/UTSWV2.uminormals.cnn" - fi - elif [[ $capture == "${index_path}/UTSWV2_2.panelplus.bed" ]] - then - normals="${index_path}/panelofnormals.panel1385V2_2.cnn" - targets="${index_path}/panel1385V2-2.cnvkit_" - elif [[ $capture == "${index_path}/hemepanelV3.bed" ]] - then - normals="${index_path}/hemepanelV3.panelofnormals.cnn" - targets="${index_path}/hemepanelV3.cnvkit_" - fi + usage fi + echo "${targets}targets.bed" echo "${targets}antitargets.bed" +echo "${normals}" source /etc/profile.d/modules.sh module load cnvkit/0.9.5 bedtools/2.26.0