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I'm having problems using the ethnicity based databases; when I put them in the function table_annovar.pl for filtering as followed:
$AnnovarPath/current/table_annovar.pl $dataPath/$sample/$sample.variants.capture.txt $AnnovarPath/humandb/ -protocol AFR.sites.2012_04,AFR.sites.2014_09,AMR.sites.2012_04,AMR.sites.2014_09,ASN.sites.2012_04,EAS.sites.2014_09,EUR.sites.2012_04,EUR.sites.2014_09,SAS.sites.2014_09,dbnsfp30a,cosmic70,gonl.snps_indels.r5.0.01,popfreq_max_20150413,snp138,snp138NonFlagged,esp6500si_all,1000g2014sep_all,cg46,snp132,bitsTrio,ILL_EM_PA_common_0.01,refGene -operation f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,g -build hg19 -nastring .
I only get dots at all positions corresponding the first 9 columns (which means the variant does not have a score in this database, eg intronic variants). I next searched for a random selection of variants in the databases, as maybe they wouldn't be in there, but I ended up finding some (including exonic) variants that did appear in the databases. The other databases do return filtering scores.
Important to mention is that when I run the script several hundreds (?) of warnings come up for all ethnicity based databases of the kind "Argument "C" isn't numeric in numeric eq (==) at /software/annovar//current/annotate_variation.pl line 2277, <DB> line 103180" (and this for all A,C,T and G bases and for various lines).
Can anybody help me with this problem?
$AnnovarPath/current/table_annovar.pl $dataPath/$sample/$sample.variants.capture.txt $AnnovarPath/humandb/ -protocol AFR.sites.2012_04,AFR.sites.2014_09,AMR.sites.2012_04,AMR.sites.2014_09,ASN.sites.2012_04,EAS.sites.2014_09,EUR.sites.2012_04,EUR.sites.2014_09,SAS.sites.2014_09,dbnsfp30a,cosmic70,gonl.snps_indels.r5.0.01,popfreq_max_20150413,snp138,snp138NonFlagged,esp6500si_all,1000g2014sep_all,cg46,snp132,bitsTrio,ILL_EM_PA_common_0.01,refGene -operation f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,g -build hg19 -nastring .
I only get dots at all positions corresponding the first 9 columns (which means the variant does not have a score in this database, eg intronic variants). I next searched for a random selection of variants in the databases, as maybe they wouldn't be in there, but I ended up finding some (including exonic) variants that did appear in the databases. The other databases do return filtering scores.
Important to mention is that when I run the script several hundreds (?) of warnings come up for all ethnicity based databases of the kind "Argument "C" isn't numeric in numeric eq (==) at /software/annovar//current/annotate_variation.pl line 2277, <DB> line 103180" (and this for all A,C,T and G bases and for various lines).
Can anybody help me with this problem?