Commit 40dc691c authored by Antony Le Béchec's avatar Antony Le Béchec


parent f1837b26
......@@ -843,7 +843,7 @@ for GP_FOLDER in $GP_FOLDER_LIST_UNIQ; do
# snpEff
if [ "$SNPEFF" != "" ] && [ -e $SNPEFF ]; then
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf: $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf.gz.tbi
$JAVA -Xmx4G -jar $SNPEFF -i vcf -classic -formatEff -o vcf $ASSEMBLY $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf.gz -stats $TMP/$GROUP/$PROJECT/dejavu.stats.snpeff.html -dataDir $SNPEFF_DATABASES > $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf
$JAVA -Xmx4G -jar $SNPEFF -i vcf -classic -formatEff -o vcf $ASSEMBLY $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf.gz -t -stats $TMP/$GROUP/$PROJECT/dejavu.stats.snpeff.html -dataDir $SNPEFF_DATABASES > $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf
" >> $MK
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