How to create custom region-based db and use it in table_annovar.pl command

[Shicheng-Guo]

Hi Prof. Wang,

Can you give a example how to create custom region-based db and use it in table_annovar.pl command together with ANNOVAR pre-prepared db. I have tried several different way and all of them are failed. The basic idea is to create some custom region-based bed-format db and use it together with avsnp154, nci60, dbnsfp30 etc.

table_annovar.pl demo.v1.avinput -thread 12 ~/janssen4/bin/annovar/humandb/ -buildver hg19 -csvout -out demo -remove -protocol bed,bed -operation r,r -bedfile hg38_cytoBand.txt,hg38_demo.txt -nastring . -otherinfo -polish -xref ~/janssen4/bin/annovar/humandb/gene_fullxref.txt

It looks ANNOVAR treat same format with different styles. For example, cytoBand cannot be took as bed and region (r) and must use cytoband and r.

Thanks.

Shicheng

[kaichop]

cytoband is a special keyword. If you want to create a region database, just create a standard BED file or generic file (five columns).

…

On Sun, May 23, 2021 at 12:22 AM Shicheng Guo ***@***.***> wrote: Hi Prof. Wang, Can you give a example how to create custom region-based db and use it in table_annovar.pl command together with ANNOVAR pre-prepared db. I have tried several different way and all of them are failed. The basic idea is to create some custom region-based bed-format db and use it together with avsnp154, nci60, dbnsfp30 etc. table_annovar.pl demo.v1.avinput -thread 12 ~/janssen4/bin/annovar/humandb/ -buildver hg19 -csvout -out demo -remove -protocol bed,bed -operation r,r -bedfile hg38_cytoBand.txt,hg38_demo.txt -nastring . -otherinfo -polish -xref ~/janssen4/bin/annovar/humandb/gene_fullxref.txt It looks ANNOVAR treat same format with different styles. For example, cytoBand cannot be took as bed and region (r) and must use cytoband and r. Thanks. Shicheng — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#142>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OD7WQSABYVO7QBDVL3TPB7KBANCNFSM45LJPLVA> .

[Shicheng-Guo]

For custom-bed format db, which protocol should be used?

Here is the command I used, however, the output don't give me expected result.

table_annovar.pl demo.v1.avinput -thread 12 ~/janssen4/bin/annovar/humandb/ -buildver hg19 -csvout -out demo -remove -protocol cytoBand,bed -operation r,r -bedfile hg38_demo.txt -nastring . -otherinfo -polish -xref ~/janssen4/bin/annovar/humandb/gene_fullxref.txt

Here is the custom-bed db,

1       10000   10002   1:10000-10002   score=1570391677
1       10001   10003   1:10001-10003   score=1570391692
1       10002   10004   1:10002-10004   score=1570391694
1       10007   10009   1:10007-10009   score=1570391698
1       10008   10010   1:10008-10010   score=1570391702
1       10014   10016   1:10014-10016   score=1570391706
1       10018   10020   1:10018-10020   score=775809821
1       10019   10021   1:10019-10021   score=1570391708
1       10020   10022   1:10020-10022   score=1570391710
1       10025   10027   1:10025-10027   score=1570391712

Here is the output:

Chr,Start,End,Ref,Alt,cytoBand,bed,Otherinfo1
1,894644,894654,T,A,.,.,""
1,10001,10001,T,A,"1p36.33","Name=NA",""
1,10002,10002,A,C,"1p36.33","Name=NA",""
1,10003,10003,A,C,"1p36.33","Name=NA",""
1,10008,10008,A,G,"1p36.33","Name=NA",""
1,10009,10009,A,G,"1p36.33","Name=NA",""
1,10015,10015,A,G,"1p36.33","Name=NA",""
1,10019,10019,TA,T,.,.,""
1,10020,10020,A,C,"1p36.33","Name=NA",""
1,10021,10021,A,G,"1p36.33","Name=NA",""
1,10026,10026,A,C,"1p36.33","Name=NA",""
1,10027,10027,A,C,"1p36.33","Name=NA",""
1,10027,10027,A,G,"1p36.33","Name=NA",""
1,10032,10032,A,C,"1p36.33","Name=NA",""
1,10033,10033,A,G,"1p36.33","Name=NA",""
1,10039,10039,A,C,"1p36.33","Name=NA",""
1,10043,10043,T,A,"1p36.33","Name=NA",""
1,10045,10045,A,C,"1p36.33","Name=NA",""
1,10045,10045,A,G,"1p36.33","Name=NA",""
1,10051,10051,A,C,"1p36.33","Name=NA",""
1,10051,10051,A,G,"1p36.33","Name=NA",""
1,10051,10051,A,AC,"1p36.33","Name=NA",""
1,10055,10055,T,TA,"1p36.33","Name=NA",""

I'd like to upload the data I used and really hope to get some help to figure out how to do it correctly.
Thanks.
Shicheng
hg38_demo.txt

demo.v1.avinput.txt
hg38_demo.txt.idx.txt
hg38_demo.txt.txt

[Shicheng-Guo]

Thanks the God! The first one succeeds.

table_annovar.pl demo.v1.avinput -thread 12 ~/janssen4/bin/annovar/humandb/ -buildver hg38 -csvout -out demo -remove -protocol bed -operation r -bedfile hg38_demo.txt -arg '-colsWanted all' -nastring . -otherinfo -polish -xref ~/janssen4/bin/annovar/humandb/gene_fullxref.txt

Chr,Start,End,Ref,Alt,bed,Otherinfo1
1,894644,894654,T,A,.,""
1,10001,10001,T,A,"Name=score=1570391677",""
1,10002,10002,A,C,"Name=score=1570391692,score=1570391677",""
1,10003,10003,A,C,"Name=score=1570391692,score=1570391694",""
1,10008,10008,A,G,"Name=score=1570391698",""
1,10009,10009,A,G,"Name=score=1570391702,score=1570391698",""
1,10015,10015,A,G,"Name=score=1570391706",""
1,10019,10019,TA,T,.,""
1,10020,10020,A,C,"Name=score=775809821,score=1570391708",""
1,10021,10021,A,G,"Name=score=1570391708,score=1570391710",""
1,10026,10026,A,C,"Name=score=1570391712",""
1,10027,10027,A,C,"Name=score=1570391712,score=1570391716",""
1,10027,10027,A,G,"Name=score=1570391712,score=1570391716",""
1,10032,10032,A,C,"Name=score=1570391720",""
1,10033,10033,A,G,"Name=score=1570391722,score=1570391720",""
1,10039,10039,A,C,"Name=score=978760828",""
1,10043,10043,T,A,"Name=score=1008829651",""
1,10045,10045,A,C,"Name=score=1570391729",""
1,10045,10045,A,G,"Name=score=1570391729",""
1,10051,10051,A,C,"Name=score=1052373574,score=1326880612",""
1,10051,10051,A,G,"Name=score=1052373574,score=1326880612",""