Commit 34576ae8 authored by Antony Le Béchec's avatar Antony Le Béchec

V20210108

parent b89cc928
......@@ -745,10 +745,10 @@ for GP_FOLDER in $GP_FOLDER_LIST_UNIQ; do
echo '##fileformat=VCFv4.1' > \$@.tmp; \
echo '#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $SAMPLE_NAME' >> \$@.tmp; \
$BGZIP -c \$@.tmp > \$@; \
rm -f \$@.tmp; \
rm -rf \$@.tmp; \
fi;
$TABIX \$@;
rm -f $<.sort.*
rm -rf $<.sort.*
" >> $MK
VCFGZ_LIST="$VCFGZ_LIST $VCF.simple.vcf.gz"
((VCFGZ_NB++))
......@@ -792,8 +792,8 @@ for GP_FOLDER in $GP_FOLDER_LIST_UNIQ; do
mkdir $<.sort.
$BCFTOOLS sort -T $<.sort. \$@.tmp.vcf | $BCFTOOLS annotate -x INFO/AN,INFO/AC,INFO/AF | $BCFTOOLS +fill-tags -- -t AN,AC,AF,AC_Hemi,AC_Hom,AC_Het,ExcHet,HWE,MAF,NS > \$@;
#rm \$@.tmp.vcf
rm \$@.tmp*
rm -f $<.sort.*
rm -rf \$@.tmp*
rm -rf $<.sort.*
" >> $MK
# --multithreading --threads=$THREADS
# --norm_options='--multiallelics=-any,--rm-dup=exact'
......@@ -864,7 +864,7 @@ for GP_FOLDER in $GP_FOLDER_LIST_UNIQ; do
echo "$TMP/$GROUP/$PROJECT/dejavu.annovar: $TMP/$GROUP/$PROJECT/dejavu.vcf
perl $ANNOVAR/convert2annovar.pl --format vcf4old --allallele --outfile \$@.tmp $<
cat \$@.tmp | cut -f1-5 > \$@
rm -f \$@.tmp
rm -rf \$@.tmp
" >> $MK
......
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