GATK's Apply Recalibration not working

Question

[Hatem Elshazly]

Hi there,

I'm having a problem using GATK's ApplyRecalibration tool using this command:

java -jar "GenomeAnalysisTK.jar" -T "ApplyRecalibration" -R human_g1k_v37.fasta -input fileContents.vcf \
    --ts_filter_level "99.9" --mode "SNP" --recal_file dataset_1139.dat_0.recal \
    --tranches_file dataset_1140.dat_0.tranches --out dataset_1142.dat_0.vcf

this is the error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name   FeatureType  Documentation
##### ERROR BCF2  VariantContext  (this is an external codec and is not documented within GATK)
##### ERROR VCF  VariantContext  (this is an external codec and is not documented within GATK)
##### ERROR VCF3  VariantContext  (this is an external codec and is not documented within GATK)
##### ERROR ------------------------------------------------------------------------------------------

I tried to look for some solutions, I added a :NAME,VCF tag before the vcf file path, I used a different version of GATK, I tried using another vcf file and I validated the vcf file I'm using, using GATK's ValidateVariants and it was validated with no problem but this problem still presists.

Any ideas or suggestion will be appreciated.

Thanks in advance.
shazly

Answer 1

[Hatem Elshazly]

Ok, Luckily I figured it out.

There is nothing wrong with the VCF file, the recal and tranches files were empty, I was mislead by the error message!

Thanks everyone.

[sunyanling]

can you tell me how to solve it? I met the same question

[Hatem Elshazly]

In my case the recal and tranches files were empty, I was using the wrong files but this is not always the cause of this error so there may be a different reason for this error in your case but from my experience you can start with checking the validity of your input files.

Answer 2

[Pierre Lindenbaum]

try '--input' instead of '-input'

and/or

--input:myvcf,VCF fileContents.vcf

and/or

try compress and index your vcf with bgzip+tabix

[Hatem Elshazly]

I tried doing that and it didn't work.

Its very weird, in the log info I get this line:

INFO  14:21:11,775 ArgumentTypeDescriptor - Dynamically determined type of fileContents.vcf.gz to be VCF

Then the error occurs.