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Merge pull request #240 from RoanKanninga/master
fix tortilla links
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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 | ||
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#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 | ||
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# merge gvcfs | ||
ml GATK/4.1.2.0-Java-1.8.0_144-unlimited_JCE | ||
ml HTSlib/1.9-foss-2015b | ||
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#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 | ||
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#java -jar $EBROOTGATK/gatk-package-4.1.2.0-local.jar GatherVcfs --help | ||
#exit 0 | ||
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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 | ||
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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 | ||
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## | ||
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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 | ||
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python gvcf2bed2.py \ | ||
-I ${INPUT} \ | ||
-O ${OUTPUT} \ | ||
-b ${bedfile} | ||
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python ${HOME}/github/ngs-utils/bin/gvcf2bed.py \ | ||
-I ${INPUT} \ | ||
-O ${OUTPUT} \ | ||
-b ${bedfile} | ||
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exit 0 | ||
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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 |
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