GATK error

[sridhar28]

Dear All,

I am using GATK for first time. i installed galaxy locally and running the softwares in it.
I am using Unified Genotyper module. my Gatk version is (GenomeAnalysisTK-2.5-2-gf57256b)
I am getting error
##### 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: The fasta file you specified (/tmp/tmp-gatk-NYjkbj) does not exist.

i mentioned the path to human genome fasta file in .loc file but again i am getting same error..

Could anyone suggest on this...

Thanks
Sridhar

[sheenams]

What is the exact command that you used?

[sridhar28]

Hi,
Actually i am running it in galaxy interface. I am using Unified Genotyper module in GATK.
in backend i got the command.

python /illumina/data/galaxy/galaxy-dist/tools/gatk/gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_266.dat" -d "-I" "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_150.dat" "bam" "gatk_input_0" -d "" "/illumina/data/galaxy/galaxy-dist/database/files/_metadata_files/000/metadata_11.dat" "bam_index" "gatk_input_0" -p 'java -jar "/illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads 4 --out "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_264.dat" --metrics_file "/illumina/data/galaxy/galaxy-dist/database/files/000/dataset_265.dat" -R "" --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0"

[newbietonextgen]

Would be easy to run the jar file than running on the Galaxy. You need to have a .dict (dictionary) file of the fasta file used for alignment. Picards tools can be used to make .dict file. You can call population level SNPs provided you have Read Groups present in the bam files.

java -jar path to Genome analysisTK -T UnifiedGenotyper -b bam file or path

Check the GATK forums or use -h to get details.

java -jar path to Genome analysisTK -T UnifiedGenotyper -h

[sridhar28]

Hi newbie,

thanks for you reply..

you mean instead of using the human genome fasta file i can use the .dict file while running the Unified Genotyper?
Also could you tell how to have "Read Groups present in the bam files." ??

i saw in galaxy interface the dbSNP file is needed?? to run the software dbSNP vcf file is not required??

[newbietonextgen]

You need both the files (fasta and .dict) to be present in the same folder/location.

Picard tools (http://picard.sourceforge.net) will help you with adding RG groups to your bam files. Use the tool AddOrReplaceReadGroups to achieve it.

You don't need a VCF file from dbSNP. If you give it, it only gives the SNP ids, telling that they have been previously found or unique. GATK can call SNPS without this file (dbSNP).

[sridhar28]

Thanks for your suggestions. after AddorReplaceGroup from picard running GATK ..

the output is like

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT human
INFO 12:23:28,619 ProgressMeter - chr1:5545193 5.55e+06 30.0 s 5.0 s 0.2% 4.6 h 4.6 h
INFO 12:23:58,620 ProgressMeter - chr1:10890877 1.09e+07 60.0 s 5.0 s 0.4% 4.7 h 4.7 h
INFO 12:24:28,621 ProgressMeter - chr1:16540257 1.65e+07 90.0 s 5.0 s 0.5% 4.7 h 4.6 h
INFO 12:24:58,622 ProgressMeter - chr1:22062765 2.21e+07 120.0 s 5.0 s 0.7% 4.7 h 4.6 h
INFO 12:25:28,623 ProgressMeter - chr1:27533021 2.75e+07 2.5 m 5.0 s 0.9% 4.7 h 4.6 h
INFO 12:25:58,624 ProgressMeter - chr1:33110681 3.31e+07 3.0 m 5.0 s 1.1% 4.7 h 4.6 h

So the VCF file will be created finally after completing all process or i should give any additional option in command line to get the VCF output??

Thanks
Sridhar