Igvtools Index "Error: For Input String: "Pass""

Question

[GPR]

Hello, I am having trouble indexing vcf files from VarScan.v2.2.11. When I try indexing in IGVTools, I get the following error: Error: For input string: "PASS" I found a thread here: Importing Varscan Vcf To Igv where the same problem is reported but a solution is not spelled out.. Can somebody help out with how to fix a vcf so that it is recognized by IGVTools? Thanks, G.

Answer 1

[Pierre Lindenbaum]

Is there a line in the VCF header like:

##FILTER=<ID=PASS,Description="...">

? if not, try to add it or replace the "PASS" in the FILTER column by "."

[GPR]

Got it, thanks!