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

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.

index
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by GPR GPR

1 answer

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 "."

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written by Pierre Lindenbaum Pierre Lindenbaum

Got it, thanks!

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written by GPR GPR

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