Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

GenomeSTRiP v2.0 CNV calling

alirezakjalirezakj Member
edited March 2015 in GenomeSTRiP

Hi Bob,

I upgraded to version 2 and ran my samples with a 30 background population samples from 1000G for DEL discovery. I know that SVToolkit now calls deletions and copy number variation, my question is; how do I run CNV discovery. Here are my commands;

java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVPreprocess.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ -cp ${classpath} \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R data/human_g1k_v37.fasta \ -genomeMaskFile data/human_g1k_v37.mask.100.fasta \ -ploidyMapFile data/humgen_g1k_v37_ploidy.map \ -copyNumberMaskFile data/cn2_mask_g1k_v37.fasta \ -genderMapFile data/geneder1000GandMysamples.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -reduceInsertSizeDistributions true \ -bamFilesAreDisjoint true \ -computeGCProfiles true \ -jobLogDir ${runDir}/logs \ -I ${bamList} \ -run \
java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVDiscovery.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ -cp ${classpath} \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R data/human_g1k_v37.fasta \ -genomeMaskFile data/human_g1k_v37.mask.100.fasta \ -genderMapFile data/geneder1000GandMysamples.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -jobLogDir ${runDir}/logs \ -minimumSize 100 \ -maximumSize 1000000 \ -suppressVCFCommandLines \ -I ${bamList} \ -O ${sites} \ -run \
java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVGenotyper.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ --disableJobReport \ -cp ${classpath} \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R data/human_g1k_v37.fasta \ -genomeMaskFile data/human_g1k_v37.mask.100.fasta \ -ploidyMapFile data/humgen_g1k_v37_ploidy.map \ -genderMapFile data/geneder1000GandMysamples.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -jobLogDir ${runDir}/logs \ -I ${bamList} \ -vcf ${sites} \ -O ${genotypes} \ -run

Would you please let me know what should I do to run CNV calling! And let me know if I did anything wrong in my DEL calling.

Thank you so much,
Reza

Best Answers

Answers

Sign In or Register to comment.