Commit 3c5280b2 authored by Antony Le Béchec's avatar Antony Le Béchec

V20210114

parent 8b7c2d53
......@@ -941,7 +941,7 @@ for GP_FOLDER in $GP_LIST_UNIQ; do
# Annotation
HOWARD_split=$(echo " ( 10000 / sqrt($NB_VCF+1) ) + 1 " | bc) # Prevent high memory
if [ "$DEJAVU_ANNOTATION" != "" ]; then
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.vcf: $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz.tbi
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf: $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz.tbi
$BCFTOOLS view $< | cut -f1-8 > $<.reduced.vcf
+$HOWARD --input=$<.reduced.vcf --output=\$@.tmp.tmp.vcf --config=$HOWARD_CONFIG --config_annotation=$HOWARD_CONFIG_ANNOTATION --annotation=$DEJAVU_ANNOTATION --calculation=$DEJAVU_CALCULATION --nomen_fields=$DEJAVU_NOMEN_FIELDS --annovar_folder=$ANNOVAR --annovar_databases=$ANNOVAR_DATABASES --snpeff_jar=$SNPEFF --snpeff_databases=$SNPEFF_DATABASES --multithreading --threads=$THREADS --snpeff_threads=$THREADS --tmp=$TMP_FOLDER_TMP --env=$CONFIG_TOOLS
$BCFTOOLS sort -T $<.sort.1. \$@.tmp.tmp.vcf > \$@.tmp.tmp.tmp.vcf
......@@ -959,19 +959,30 @@ for GP_FOLDER in $GP_LIST_UNIQ; do
" >> $MK
else
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.vcf: $TMP/$GROUP/$PROJECT/dejavu.simple.vcf
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.howard.vcf: $TMP/$GROUP/$PROJECT/dejavu.simple.vcf
cp $TMP/$GROUP/$PROJECT/dejavu.simple.vcf $TMP/$GROUP/$PROJECT/dejavu.annotated.vcf
" >> $MK
fi;
# snpEff
# snpEff classic
if [ "$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 -t -stats $TMP/$GROUP/$PROJECT/dejavu.stats.snpeff.html -dataDir $SNPEFF_DATABASES > $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf: $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz.tbi
$JAVA -Xmx4G -jar $SNPEFF -i vcf -classic -formatEff -o vcf $ASSEMBLY $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz -t -stats $TMP/$GROUP/$PROJECT/dejavu.stats.snpeff.html -dataDir $SNPEFF_DATABASES > $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf
" >> $MK
else
echo "$TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf: $TMP/$GROUP/$PROJECT/dejavu.simple.vcf
$BCFTOOLS view $TMP/$GROUP/$PROJECT/dejavu.simple.vcf.gz > $TMP/$GROUP/$PROJECT/dejavu.annotated.eff.vcf
" >> $MK
fi;
# Annotated
echo "$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
" >> $MK
# echo "$TMP/$GROUP/$PROJECT/VCF_LIST: $VCFGZ_LIST
# ls $^ > $TMP/$GROUP/$PROJECT/VCF_LIST
......
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