Merge pull request #221 from RoanKanninga/master

skip NC_001422.1 chromosome in gnomAD check since it doesnot exist
molgenis · Nov 23, 2018 · 20e42ea · 20e42ea
2 parents 7d0e118 + 21ab1f6
commit 20e42ea
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/protocols/AnnotateVcf.sh b/protocols/AnnotateVcf.sh
@@ -75,9 +75,9 @@ then
 		then
 			echo -e "\n[[annotation]]\nfile=\"${gnomADGenomesAnnotation}/gnomad.genomes.r2.0.2.sites.chrX.normalized.vcf.gz\"\nfields=[\"AF_POPMAX\",\"segdup\"]\nnames=[\"gnomAD_genome_AF_MAX\",\"gnomAD_genome_RF_Filter\"]\nops=[\"self\",\"self\"]" >> "${vcfAnnoGnomadGenomesConf}"
 			echo -e "\n[[annotation]]\nfile=\"${gonlAnnotation}/gonl.chrX.release4.gtc.vcf.gz\"\nfields=[\"AC\",\"AN\"]\nnames=[\"GoNL_AC\",\"GoNL_AN\"]\nops=[\"self\",\"first\"]" >> "${vcfAnnoGnomadGenomesConf}"
-		elif [[ ${batchID} == *"Y"* || ${batchID} == *"MT"* ]]
+		elif [[ ${batchID} == *"Y"* || ${batchID} == *"NC_001422.1"* ||  ${batchID} == *"MT"* ]]
 		then
-			echo "chromosome Y/MT is not in gnomAD, do nothing"
+			echo "chromosome Y/MT/NC_001422.1 is not in gnomAD, do nothing"
 		else
 			echo -e "\n[[annotation]]\nfile=\"${gnomADGenomesAnnotation}/gnomad.genomes.r2.0.2.sites.chr${batchID}.normalized.vcf.gz\"\nfields=[\"AF_POPMAX\",\"segdup\"]\nnames=[\"gnomAD_genome_AF_MAX\",\"gnomAD_genome_RF_Filter\"]\nops=[\"self\",\"self\"]" >> "${vcfAnnoGnomadGenomesConf}"
 			echo -e "\n[[annotation]]\nfile=\"${gonlAnnotation}/gonl.chrCombined.snps_indels.r5.vcf.gz\"\nfields=[\"AC\",\"AN\"]\nnames=[\"GoNL_AC\",\"GoNL_AN\"]\nops=[\"self\",\"first\"]" >> "${vcfAnnoGnomadGenomesConf}"