I am using GATK UnifiedGenotyper on multiple bam files for target enrichment sequencing. I get an error which although is a "user error", I can't seem to work it out! Any help would be greatly appreciated.
I am using Bam files that have been reduced by ReduceReads, I have many bam files, but even when I try the command with just a few I get the same error. Here is an example;
java -Xmx20g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper \
-R human_g1k_v37.fasta \
-D dbsnp_131_b37.final.rod \
-L baitgroupfile.picard \
-I sample1.reduced.bam \
-I sample2.reduced.bam \
-I sample3.reduced.bam \
-o out.vcf \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-G Standard \
-metrics out.metrics
here is the error;
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.4-3-g2a7af43):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### 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 a
n explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BCF2 VariantContext http://www.broadinstitute.org/gatk/g...BCF2Codec.html
##### ERROR VCF VariantContext http://www.broadinstitute.org/gatk/g..._VCFCodec.html
##### ERROR VCF3 VariantContext http://www.broadinstitute.org/gatk/g...VCF3Codec.html
I am using Bam files that have been reduced by ReduceReads, I have many bam files, but even when I try the command with just a few I get the same error. Here is an example;
java -Xmx20g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper \
-R human_g1k_v37.fasta \
-D dbsnp_131_b37.final.rod \
-L baitgroupfile.picard \
-I sample1.reduced.bam \
-I sample2.reduced.bam \
-I sample3.reduced.bam \
-o out.vcf \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-G Standard \
-metrics out.metrics
here is the error;
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.4-3-g2a7af43):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### 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 a
n explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BCF2 VariantContext http://www.broadinstitute.org/gatk/g...BCF2Codec.html
##### ERROR VCF VariantContext http://www.broadinstitute.org/gatk/g..._VCFCodec.html
##### ERROR VCF3 VariantContext http://www.broadinstitute.org/gatk/g...VCF3Codec.html
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