From d5b8a01a1b2534b3af7bfeabc8c80e05434d2ec8 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 12 Nov 2021 11:23:06 +0100 Subject: [PATCH] fix tortilla links --- bin/convertDos2Unix.sh | 0 bin/gVCF2BED.bash | 88 ++++++++++++++++++++++++++++++++++++++++++ bin/pseudo_bam.sh | 19 +++++---- bin/tortilla.sh | 14 +++---- 4 files changed, 106 insertions(+), 15 deletions(-) create mode 100644 bin/convertDos2Unix.sh create mode 100644 bin/gVCF2BED.bash diff --git a/bin/convertDos2Unix.sh b/bin/convertDos2Unix.sh new file mode 100644 index 0000000..e69de29 diff --git a/bin/gVCF2BED.bash b/bin/gVCF2BED.bash new file mode 100644 index 0000000..491ea56 --- /dev/null +++ b/bin/gVCF2BED.bash @@ -0,0 +1,88 @@ +INPUT=/groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.merged.g.vcf.gz +OUTPUT=/groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-22.variant.calls.bed + +#bedfile=/groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/targets.bed +#bedfile=/groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/ONC_3183841_+en-20_target_v1.bed +#bedfile=/groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/Exoom_target_v1plus50.chr22.big.bed +bedfile=/groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/Exoom_target_v1plus50.part.bed + +# merge gvcfs +ml GATK/4.1.2.0-Java-1.8.0_144-unlimited_JCE +ml HTSlib/1.9-foss-2015b + +#for b in "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "Xp" "Xnp" "Y" "MT" "NC_001422.1" +#do +# if [ -f "//groups/umcg-atd//tmp04//tmp//QXTR_276-Exoom_v1/run01//QXTR_276-Exoom_v1.batch-${b}.variant.calls.snpeff.vcf" ] +# then +# array_contains INPUTS "--variant //groups/umcg-atd//tmp04//tmp//QXTR_276-Exoom_v1/run01//QXTR_276-Exoom_v1.batch-${b}.variant.calls.snpeff.vcf" || INPUTS+=("--variant //groups/umcg-atd//tmp04//tmp//QXTR_276-Exoom_v1/run01//QXTR_276-Exoom_v1.batch-${b}.variant.calls.snpeff.vcf") +# fi +#done + +#java -jar $EBROOTGATK/gatk-package-4.1.2.0-local.jar GatherVcfs --help +#exit 0 + +java -jar $EBROOTGATK/gatk-package-4.1.2.0-local.jar GatherVcfs \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-2.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-3.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-4.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-5.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-6.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-7.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-8.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-9.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-10.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-11.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-12.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-13.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-14.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-15.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-16.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-17.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-18.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-19.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-20.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-21.variant.calls.g.vcf.gz \ +--INPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.batch-22.variant.calls.g.vcf.gz \ +--OUTPUT /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.merged.g.vcf.gz + +tabix -p vcf /groups/umcg-atd/tmp04/projects/QXTR_276-Exoom_v1/run01/results/variants/gVCF/20182579_2021287_DNA110503_509403_QXTR276_S07604514.merged.g.vcf.gz + + +## + + + +module load Python/3.6.3-foss-2015b +#export PYTHONPATH='/home/umcg-gvdvries/tools/:$PYTHONPATH' +#export PYTHONPATH='/home/umcg-gvdvries/test2/:$PYTHONPATH' +export PYTHONPATH='/groups/umcg-atd/tmp04/umcg-rkanninga/python_packages_gerben/tools/:$PYTHONPATH' +echo $PYTHONPATH + +python gvcf2bed2.py \ +-I ${INPUT} \ +-O ${OUTPUT} \ +-b ${bedfile} + +python ${HOME}/github/ngs-utils/bin/gvcf2bed.py \ +-I ${INPUT} \ +-O ${OUTPUT} \ +-b ${bedfile} + + +exit 0 + +optional arguments: + -h, --help show this help message and exit + -I INPUT, --input INPUT + Input gVCF + -O OUTPUT, --output OUTPUT + Output bed file + -s SAMPLE, --sample SAMPLE + Sample name in VCF file to use. Will default to first + sample (alphabetically) if not supplied + -q QUALITY, --quality QUALITY + Minimum genotype quality (default 20) + -nq NON_VARIANT_QUALITY, --non-variant-quality NON_VARIANT_QUALITY + Minimum genotype quality for non-variant records + (default 20) + -b, --bedgraph Output in bedgraph mode \ No newline at end of file diff --git a/bin/pseudo_bam.sh b/bin/pseudo_bam.sh index eca8737..934906e 100755 --- a/bin/pseudo_bam.sh +++ b/bin/pseudo_bam.sh @@ -22,7 +22,7 @@ function reheader(){ mv -v "${workDir}/tmp/${pseudo}.reheader.bam" "${workDir}/output/${pseudo}.bam" touch "${workDir}/${sampleName}.finished" fi - + } function showHelp() { @@ -176,19 +176,22 @@ then fi mkdir -p "${workDir}"/{input,tmp,output} - mv "${input}/"*".bams" "${workDir}/input/" + rsync -av "${input}/"*".bam" "${workDir}/input/" module load SAMtools while read line do oldKey=$(echo "${line}" | awk '{print $1}') ## DNA12345 pseudo=$(echo "${line}" | awk '{print $2}') ##sample1 - bam=$(ls "${workDir}/input/"*"${oldKey}"*".bam") ## 20000_DNA12345_000_12312.merged.bam - fileName=$(basename "${bam}") ## 20000000_DNA12345_0000000_1231244 - sampleName=${fileName%%.*} ## 20000000_DNA12345_0000000_1231244 - echo "BAM: ${bam} ${oldKey} ${pseudo} ${sampleName}" - - reheader "${workDir}" "${sampleName}" "${fileName}" "${pseudo}" + if [[ -f "${workDir}/input/"*"${oldKey}"*".bam" ]] + then + bam=$(ls "${workDir}/input/"*"${oldKey}"*".bam") ## 20000_DNA12345_000_12312.merged.bam + fileName=$(basename "${bam}") ## 20000000_DNA12345_0000000_1231244 + sampleName=${fileName%%.*} ## 20000000_DNA12345_0000000_1231244 + echo "BAM: ${bam} ${oldKey} ${pseudo} ${sampleName}" + reheader "${workDir}" "${sampleName}" "${fileName}" "${pseudo}" + else + echo "bam is not found" done<"${mapping}" fi diff --git a/bin/tortilla.sh b/bin/tortilla.sh index 07377c2..8e3f4ee 100755 --- a/bin/tortilla.sh +++ b/bin/tortilla.sh @@ -33,33 +33,33 @@ fi if [[ "${1}" == "--makeSamplesheet" || "${1}" == "-m" ]] then shift - ${EBROOTNGSMINUTILS}/tortilla_makeSamplesheet.sh ${@} + ${EBROOTNGSMINUTILS}/bin/tortilla_makeSamplesheet.sh ${@} elif [[ "${1}" == "--bamout" || "${1}" == "-b" ]] then shift - ${EBROOTNGSMINUTILS}/bamout.sh ${@} + ${EBROOTNGSMINUTILS}/bin/bamout.sh ${@} elif [[ "${1}" == "--countCoverage" || "${1}" == "-c" ]] then shift - ${EBROOTNGSMINUTILS}/countCoverage.sh ${@} + ${EBROOTNGSMINUTILS}/bin/countCoverage.sh ${@} elif [[ "${1}" == "--vcfCompare" || "${1}" == "-v" ]] then shift - ${EBROOTNGSMINUTILS}/vcf-compare_2.0.sh ${@} + ${EBROOTNGSMINUTILS}/bin/vcf-compare_2.0.sh ${@} elif [[ "${1}" == "--validateNGS" || "${1}" == "-n" ]] then shift - ${EBROOTNGSMINUTILS}/checkValidationNGS_DNA_v2.sh ${@} + ${EBROOTNGSMINUTILS}/bin/checkValidationNGS_DNA_v3.sh ${@} elif [[ "${1}" == "--revertBamToFastQ" || "${1}" == "-r" ]] then - ${EBROOTNGSMINUTILS}/revertFromBamToFastQ.sh ${@} + ${EBROOTNGSMINUTILS}/bin/revertFromBamToFastQ.sh ${@} elif [[ "${1}" == "--calculateCoverage" || "${1}" == "-cc" ]] then ${EBROOTNGSMINUTILS}/coverage_calc.sh ${@} elif [[ "${1}" == "--cramToBam" || "${1}" == "-d" ]] then - ${EBROOTNGSMINUTILS}/CramConversion.sh ${@} + ${EBROOTNGSMINUTILS}/bin/CramConversion.sh ${@} fi