Hey, I have a VCF format variant table produced by GATK pipeline which includes two controls and one clinical affected sample. By using selectvariant tool, it is very easy to reduce variants of the affected sample by comparing it with other two controls. However, I need to go further to reduce these variants by combining them with SNPdb from Sanger or NCBI. I downloaded a SNPdb file with genotypes of more than 10 other controls from Sanger (VCF format). I have resorted the chromosome order to make it the same as my variant file. I tried to use Annovar to filter these variants by combing with SNPdb but it did not work. My variant files are coming from non-human genome. Then I tried to combine variants of my file with SNPdb by using combinevariant tool of GATK. it did not work either.
Now, I need your suggestion that how can i compare the variants with extra variants from SNPdb?
Thank you
please define " but it did not work" and "it did not work either."
Sorry for not explaining it clearly. When I used annovar Variants_Reduction tool, for my case for mouse genome. It needs mouse snpdb under annovar database file but Annovar does not provide it. Then i download snpdb from NIBI or Sanger, however, the tools did not recognize it.
As for the CombineVariants tool of GATK. I used the commands as follows ( java -Xmx2g -jar GenomeAnalysisTK.jar -R genome.fa -T CombineVariants --variant myvariants.vcf --variant snpdb.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY.
It showed as ERROR MESSAGE: For input string: "."