ERROR in Running with system command <coding_change.pl

[lincj1994]

HI, I was running InterVar on the ex1.avinput. An error was reported like this: Can't exec "coding_change.pl": No such file or directory at ./table_annovar.pl line 455.

Here is the line 455 of table_annovar.pl: system ($sc) and die "Error running system command: <$sc>\n";

Any help is appreciated.

[kaichop]

depending on whether you are using Windows or Linux or Mac, it could be a PATH set up issue. You can try add ANNOVAR directory to your PATH so the program can be executed.

On Thu, Apr 15, 2021 at 8:54 AM Caijin Lin @.***> wrote:

HI, I was running InterVar on the ex1.avinput. An error was reported like this: Can't exec "coding_change.pl": No such file or directory at ./ table_annovar.pl line 455.

Here is the line 455 of table_annovar.pl: system ($sc) and die "Error running system command: <$sc>\n";

Any help is appreciated.

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[lincj1994]

@kaichop Thanks. I have another question about the input type. In the article of "InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines", it stated that "The runtime can be greatly reduced to <5 min (~0.1 ms per variant) if an existing ANNOVAR annotation file is already available". I dont know which argument was used to specify the input that has already been annotated by ANNOVAR.

[quanliustc]

You can add:

--skip_annovar      Skip the Annovar annotation, this can be true only

                    after you  already got the annovar's annotation

                    results

also please check the manual to make this work no problem.

Best,

Quan LI, Ph.D

http://www.quanli.org

[lincj1994]

You can add: … --skip_annovar Skip the Annovar annotation, this can be true only after you already got the annovar's annotation results also please check the manual to make this work no problem. Best, Quan LI, Ph.D http://www.quanli.org

Thanks for the reply. Besides, the intervar requires the input file to include Chr, Position_Start, Position_End, Reference_allele, and Alternative_allele only. But I have an input file which contains tumor_sample_barcode also, I dont know how to keep the column of tumor_sample_barcode in the output.

[quanliustc]

you can put in in the six column, then this information will be in the last column as "Otherinfo" in the final output.

[lincj1994]

you can put in in the six column, then this information will be in the last column as "Otherinfo" in the final output.

I have put it in the sixth column. But in the final output, the "Otherinfo" column contains Chromosome only, same as Column one.

[quanliustc]

set the input file as tab-separated , and also make sure you chromosome name start as chr not Chr

[lincj1994]

set the input file as tab-separated , and also make sure you chromosome name start as chr not Chr

Thank you. My input file is .tsv. The input file is organized as the example provided by InterVar, no column name and no "chr" or "Chr" as the prefix before the chromosome name. Here are the first five rows of my input and the six columns represent chromosome, start, end, Ref, Alt, sample barcode:

1 | 2116360 | 2116360 | G | T | 2002798 1 | 9775906 | 9775906 | G | C | 2000934 1 | 9777168 | 9777168 | T | G | 2001877 1 | 11188610 | 11188610 | C | CACTGGTT | 1800215 1 | 11293545 | 11293545 | C | A | 1801028 1 | 16254585 | 16254585 | G | A | 1800612

[lincj1994]

set the input file as tab-separated , and also make sure you chromosome name start as chr not Chr

Thank you. My input file is .tsv. The input file is organized as the example provided by InterVar, no column name and no "chr" or "Chr" as the prefix before the chromosome name. Here are the first five rows of my input and the six columns represent chromosome, start, end, Ref, Alt, sample barcode:

1 | 2116360 | 2116360 | G | T | 2002798 1 | 9775906 | 9775906 | G | C | 2000934 1 | 9777168 | 9777168 | T | G | 2001877 1 | 11188610 | 11188610 | C | CACTGGTT | 1800215 1 | 11293545 | 11293545 | C | A | 1801028 1 | 16254585 | 16254585 | G | A | 1800612

Also, I've tried the input below and the Otherinfo column still didnt include the sample barcode. chr1 | 2116360 | 2116360 | G | T | 2002798 chr1 | 9775906 | 9775906 | G | C | 2000934 chr1 | 9777168 | 9777168 | T | G | 2001877 chr1 | 11188610 | 11188610 | C | CACTGGTT | 1800215 chr1 | 11293545 | 11293545 | C | A | 1801028 chr1 | 16254585 | 16254585 | G | A | 1800612

[quanliustc]

I think I found the reason why your sample information lost:

As Annovar’s output changed the sample information column name from “Otherinfo” to “Otherinfo1”.

Will revise this.

Best,

Quan LI, Ph.D

http://www.quanli.org

[quanliustc]

Otherinfo1 or Otherinfo are fixed.

[lincj1994]

Otherinfo1 or Otherinfo are fixed.

Hi. CancerVar has the same problem.