Commit 850b49a0 authored by Antony Le Béchec's avatar Antony Le Béchec

Merge branch '0.9.18.2'

parents efec23fd 96f6f5d7
......@@ -978,7 +978,8 @@ for GP_FOLDER in $GP_LIST_UNIQ; do
# Annotated
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.vcf: $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf.gz.tbi $TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf.gz.tbi
$BCFTOOLS concat $TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf.gz --allow-overlaps --threads $THREADS > $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf
#$BCFTOOLS concat $TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf.gz --allow-overlaps --threads $THREADS > $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf
$BCFTOOLS annotate -a $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf.gz -c EFF $TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf.gz --threads $THREADS --single-overlaps -k > $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf
" >> $MK
......
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