Genomestrip Generate Haploid CNV Genotypes

Question

[willgilks]

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.

Answer 1

[willgilks]

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/