I am trying to compare the results of INDELS from VarScan2 and Lofreq. Lofreq is already treated for false positives internally but to compare I should be also filtering out the false positives from VarScan2 output. The fpfilter.pl (old) does not work with the INDEL vcf4.1 format file of VarScan2 output. The perl module developed at WashU for INDELS has got dependencies so am not intending to use it, as am not very familiar with usage of perl module and also there is not much documentation of how to use that falsefilterindels.pm and so am not being able to understand it very clearly. Is there any script which I can use to filter the false positive indels from my varscan indels output data or did WashU make any compatible script like that of fpfilter.pl for INDELS. I tried searching but could not find one. I appreciate any kind of suggestions from the community.
