Question: Using SSrGE for SNV calling
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gravatar for landscape95
13 months ago by
landscape95160
landscape95160 wrote:

Hi everyone, I came across the paper of of Olivier et. al. https://www.nature.com/articles/s41467-018-07170-5 and here I apply the package SSrGE for SNV calling https://github.com/lanagarmire/SSrGE. I used GATK3 for SNV calling. Here is my code for debugging:

/usr/lib/jvm/java-8-oracle/jre/bin/java -Xmx110g -jar /home/joe/Tools/GATK3/GenomeAnalysisTK.jar -T SplitNCigarReads -I /home/joe/SSrGEoutput/SSrGE_1st_test/snv_pipeline_results/tmp/17689/dedupped.bam -o /home/joe/SSrGEoutput/SSrGE_1st_test/snv_pipeline_results/tmp/17689/split.bam -R /home/joe/Tools/hg19ref/GRCh37.p13.genome.fa -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS --fix_misencoded_quality_score

and I got this error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): 
##### 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 https://software.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: Argument with name 'fix_misencoded_quality_score' isn't defined.
##### ERROR ------------------------------------------------------------------------------------------

The error is in this argument fix_misencoded_quality_score but as I have searched online, this command exists with GATK3. https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_engine_CommandLineGATK.php I have no idea how to solve this problem, has anyone experienced this problem?

Your help is really appreciated!

snv ssrge • 399 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by landscape95160
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