teone182
commented
1 year ago I've just realised that one quick solution is to replace all the 0 values in the in-house annotation file with 0.0 . Like this, table_annovar.pl works fine and the 0 values are basically not lost. However, a more structured solution implemented in the script would be much appreciated. Thanks again!
Hi there!
I'm using table_annovar.pl to annotate some variants with some in-house annotation values. This step comes after employing convert2annovar.pl to convert a vcf file into an Annovar-specific input file. So, this is the code I'm using:
1) $Annovar/convert2annovar.pl -format vcf4 $WorkFolder/MyFile_Start.vcf.gz -outfile MyFile.input -allsample -withfreq -include 2> Annovar.log
2) $Annovar/table_annovar.pl MyFile.input $Annovar/humandb/ --buildver hg19 -out MyFile -remove -protocol refGene,testAnno -operation g,f --argument '--neargene 2000, --neargene 2000' --thread 40 --maxgenethread 40 -nastring . >> Annovar.log
An example of the first lines (plus header) of the hg19_testAnno.txt is the following:
Chr Start End Ref Alt MyAnno
chr5 13591 13591 A G 0.127 chr5 13604 13604 C G 1.156
While all the MyAnno numerical values, as well as the missing values, are correctly annotated in the MyFile.hg19_multianno.txt file, MyAnno values equal to 0 are wrongly annotated as missing values in the output file. Any help with this?
Thanks a lot in advance!
Matteo