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annovar.sh
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annovar.sh
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# Author: Julie BOGOIN
source ~/miniconda3/etc/profile.d/conda.sh
conda activate annot_env
echo ""
echo "*******************"
echo "annotation.sh start"
echo "*******************"
echo ""
rm -Rf annovar_output
mkdir -p annovar_output
## Download annotation databases from ANNOVAR or UCSC and save to humandb/ directory
#perl ./annotate_variation.pl -downdb avdblist
#perl annotate_variation.pl -downdb -buildver hg38 -webfrom annovar refGene humandb
## Retirer les noms de colonnes au fichier interval_results.txt > /annovar_output/ex1.avinput
sed '1d' cnv_with_frequences.txt > ex1.avinput
## Remplacer XF par X et XM par X
sed -i -e "s/XF/X/g" ex1.avinput
sed -i -e "s/XM/X/g" ex1.avinput
sudo perl ~/annovar/table_annovar.pl \
ex1.avinput \
~/annovar/humandb \
--buildver hg38 \
--out annotation \
--remove \
--otherinfo \
--protocol refGene \
--operation g
mv ex1.avinput annovar_output/
mv annotation.hg38_multianno.txt annovar_output/
#first output file: .variant_function
#contains annotation for all variants, by adding two columns to the beginning of each input line
#second output file: .exonic_variant_function
#contains the amino acid changes as a result of the exonic variant.
echo ""
echo "annotation.sh job done!"
echo ""