Shicheng-Guo
commented
3 years ago Okay. Great day!!! Congratulation!!!
table_annovar.pl demo.v1.avinput -thread 12 ~/janssen4/bin/annovar/humandb/ -buildver hg38 -csvout -out demo -remove -protocol bed,cytoBand,dbnsfp30a -operation r,r,f -bedfile hg38_demo.txt -arg '-colsWanted 5','-colsWanted 3',"-colsWanted all" -nastring . -otherinfo -polish -xref ~/janssen4/bin/annovar/humandb/gene_fullxref.txt
Looks grasp is okay
table_annovar.pl demo.avinput -thread 1 ~/janssen4/bin/annovar/humandb/ -buildver hg38 -csvout -out demo -remove -protocol bed -operation r -bedfile hg38_grasp.txt -arg '-colsWanted all' -nastring . -otherinfo -polish -xref ~/janssen4/bin/annovar/humandb/gene_fullxref.txt
Still error but should be closed, how to solve the problem:
cd /home/sguo2/janssen4/db/grasp2
perl grasp2annovar.pl > hg38_grasp.txt
cp hg38_grasp.txt hg38_grasp2.txt
perl -p -i -e '{s/g.s/gs/g}' hg38_grasp2.txt
perl -p -i -e '{s/h.e/he/g}' hg38_grasp2.txt
perl -p -i -e '{s/\<//g}' hg38_grasp2.txt
perl -p -i -e '{s/\>//g}' hg38_grasp2.txt
perl -p -i -e '{s/Cloninger.s/Cloningers/g}' hg38_grasp2.txt
perl -p -i -e '{s/=10E4.l-Liver/=10E4ul-Liver/g}' hg38_grasp2.txt
perl -p -i -e '{s/Fuchs.s/Fuchss/g}' hg38_grasp2.txt
grep -a l-Liver hg38_grasp2.txt
grep -a Fuchs hg38_grasp2.txt
perl ~/janssen4/bin/annovar/index_annovar.pl hg38_grasp2.txt -bin 1000 -outfile ~/janssen4/bin/annovar/humandb/hg38_grasp.txt
############################################################
mkdir split
cp hg38_grasp2.txt split
cd split
split -l 500 hg38_grasp2.txt
for i in `ls x*`
do
perl ~/janssen4/bin/annovar/index_annovar.pl $i -bin 10 -outfile ./demo.$i
done
Great. Now cytoBand is added when '-colsWanted 3' is set