Commit ab11d78b authored by Antony Le Béchec's avatar Antony Le Béchec

Merge branch '0.9.18.2'

parents d301fd5e bbb8a358
......@@ -859,7 +859,7 @@ for GP_FOLDER in $GP_LIST_UNIQ; do
#$JAVA -jar $PICARD FixVcfHeader -I $< -O $<.tmp.fixed.vcf;
#cp $< $<.tmp.fixed.vcf;
#zcat $<.tmp.fixed.vcf | grep -v '^##Prioritize list is' | sed s/Number=R/Number=./g | sed s/Number=G/Number=./g > $<.tmp.fixed2.vcf;
zcat $< | grep -v '^##Prioritize list is' | sed s/Number=R/Number=./g | sed s/Number=G/Number=./g > $<.tmp.fixed2.vcf;
zcat $< | grep -v '^##Prioritize list is' | sed s/Number=R/Number=./g | sed s/Number=G/Number=./g | $BCFTOOLS sort -T $<.sort2. > $<.tmp.fixed2.vcf;
$BGZIP -c $<.tmp.fixed2.vcf > $<.tmp.fixed.vcf.gz;
$TABIX $<.tmp.fixed.vcf.gz
if $BCFTOOLS annotate -x FILTER,QUAL,ID,INFO $<.tmp.fixed.vcf.gz 1>/dev/null 2>/dev/null; then \
......
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