Genomestrip Generate Haploid CNV Genotypes
1
0
Entering edit mode
7.8 years ago
willgilks ▴ 360

I'm trying to generate haploid CNV genotypes on the output of GenomeStrip's CNV Discovery Pipeline.

My code is:

    vcf_path=results
    vcf=gs_cnv.genotypes.vcf
    ref_seq=../reference_data/dm6.fa
    ploidy=../reference_data/ploidy_dm6.map
    gender_map=../reference_data/gstrip_lhm_rg_gender.map


    SV_TMPDIR=./tmpdir
    SV_DIR=/cm/shared/apps/svtoolkit/2.0.1602/


     which java > /dev/null || exit 1
        which Rscript > /dev/null || exit 1
        which samtools > /dev/null || exit 1

            export PATH=${SV_DIR}/bwa:${PATH}
            export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}

    mx="-Xmx4g"
    classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"

java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar

java -Xmx4g -cp ${classpath} ${mx} org.broadinstitute.sv.apps.GenerateHaploidCNVGenotypes \
    -R ${ref_seq} \
    -vcf ${vcf_path}/${vcf} \
    -O lhm_rg_cnvGenos_raw.vcf \
        -ploidyMapFile ${ploidy} \
        -genderMapFile ${gender_map} \
        -estimateAlleleFrequencies true \
        -genotypeLikelihoodThreshold 0.001 \
            -debug true \
            --verbose true || exit

My platform is Linux Sun Grid Engine. My GenomeStrip is SVToolkit version 2.00 (build 1602), Build date: 2015/07/21 09:43:14

The error message is:

Exception in thread "main" java.lang.RuntimeException: Cannot locate R script: genotyping/estimate_cnv_allele_frequencies.R (SV_DIR = /cm/shared/apps/svtoolkit/2.0.1602/)

I can't find this R script in the Genomestrip folders, which would lead me to assume that this is why the script isn't working but I could be wrong. I'm wondering if my variables are correct. I have asked about this on the GATK Genomestrip forum and it was suggested to do export SVDIR-= but this doesn't seem to work either, in various arrangements.

Any help would be most appreciated.

cnv genomestrip generatehaploidcnvgenotypes • 1.7k views
ADD COMMENT
0
Entering edit mode
7.8 years ago
willgilks ▴ 360

From GATK Genomestrip/2.0 forum, the R script has not been included in the current version, but is available from ftp://ftp.broadinstitute.org/pub/svtoolkit/misc/cnvs/ and should be copied into ${SV_DIR}/R/genotyping/

ADD COMMENT

Login before adding your answer.

Traffic: 2384 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6