The dbSNP 142 file is not found.

[shangyf-stu]

Dear sir,
Thanks for your good job!
I just finish instructing the pipeline. But when I run ISOWN with the test data you provide for us, there is an error.
`annotating input file with ANNOVAR ...

The dbSNP 142 file is not found. Please correct the path in /software/pipeline/somatic_call/ISOWN/ISOWN/bin/database_annotation.pl and try again - see path below:

/software/pipeline/somatic_call/ISOWN/ISOWN/bin/../external_databases/dbSNP142_All_20141124.vcf.gz.modified.vcf.gz`

I am sure I have done everything followed your course, and I have tried to download dbSNP and re-format it again.
But I still couldn't find dbSNP142_All_20141124.vcf.gz.modified.vcf.gz

Any help is grateful.

Best wishes,
Shang

[shangyf-stu]

After re-format, I got three files named
00-All.modified.vcf.gz, 00-All.modified.vcf.gz.tbi, 00-All.vcf.gz
And there is no error message.

[groadabike]

Yeah, I had the same error as @shangyf-stu. In file database_annotation.pl says

my $dbSNP_142="$cwd/../external_databases/dbSNP142_All_20141124.vcf.gz.modified.vcf.gz";

I changed it to

my $dbSNP_142="$cwd/../external_databases/00-All.modified.vcf.gz";