Hi all,
I sequenced transcriptome of 7 samples including 3 from one environment and the other 4 from another environment. I did de novo assembly and want to call SNPs using GATK. I merged the unigenes as a reference and now I plan to call the SNP from each sample. There is no reference genome neither knownSites of SNPs.
The command lines I used are listed below:
1. java -jar GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R mergeunigene_ref.fa -T RealignerTargetCreator -I sample1_dedup.bam -o sample1.intervals
2. java -jar GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R mergeunigene_ref.fa -T IndelRealigner -targetIntervals sample1.intervals -I sample1_dedup.bam -o sample1_deduprealn.bam
It runs well till here, but when I run BaseRecalibrator, Error is below:
3. java -jar GenomeAnalysisTK-2.5-2-gf57256b/Genome
AnalysisTK.jar -R mergeunigene_ref.fa -T BaseRecalibrator -I sample1_deduprealn7.bam -o sample1.grp
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
##### 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: This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.
Does anybody meet this problem? Any comment is appreciated.
I sequenced transcriptome of 7 samples including 3 from one environment and the other 4 from another environment. I did de novo assembly and want to call SNPs using GATK. I merged the unigenes as a reference and now I plan to call the SNP from each sample. There is no reference genome neither knownSites of SNPs.
The command lines I used are listed below:
1. java -jar GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R mergeunigene_ref.fa -T RealignerTargetCreator -I sample1_dedup.bam -o sample1.intervals
2. java -jar GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R mergeunigene_ref.fa -T IndelRealigner -targetIntervals sample1.intervals -I sample1_dedup.bam -o sample1_deduprealn.bam
It runs well till here, but when I run BaseRecalibrator, Error is below:
3. java -jar GenomeAnalysisTK-2.5-2-gf57256b/Genome
AnalysisTK.jar -R mergeunigene_ref.fa -T BaseRecalibrator -I sample1_deduprealn7.bam -o sample1.grp
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
##### 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: This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.
Does anybody meet this problem? Any comment is appreciated.
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