Question: GATK VariantFiltration NumberFormatException
gravatar for ajaypaulsharma
11 months ago by
ajaypaulsharma0 wrote:


I am trying to filter a vcf file Info column. I have some Info Fields with values "DP=.". When I try to use GATK VariationFilter tool with option -filter "DP>50", it throws error: java.lang.NumberFormatException for input string ".". This is the case with many other values in INFO Column in vcf file. I also tried using -filter "DP!='.' && DP>50". How can I overcome this issue?

Thanks! Ajay

ADD COMMENTlink modified 11 months ago by Brice Sarver3.5k • written 11 months ago by ajaypaulsharma0
gravatar for Brice Sarver
11 months ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

The GATK is particularly sensitive to type, and you can get weird results if you try to mix-and-match among them. Perhaps the more relevant question is why your DP fields are ''. If you don't have a depth of at least 1, how do you have any evidence for that site to potentially harbor a variant in the first place?

A quick workaround that should cause GATK to exit cleanly would be to replace these strings with DP=0, and then your filter should work. Something like sed is your friend here and will be quite fast.

ADD COMMENTlink written 11 months ago by Brice Sarver3.5k
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