fix tortilla links

molgenis · Nov 12, 2021 · d5b8a01 · d5b8a01
1 parent e450b01
commit d5b8a01
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Showing 4 changed files with 106 additions and 15 deletions.
diff --git a/bin/convertDos2Unix.sh b/bin/convertDos2Unix.sh
diff --git a/bin/gVCF2BED.bash 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 ${bedfile} 
+
+
+exit 0
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -I INPUT, --input INPUT
+                        Input gVCF
+  -O OUTPUT, --output OUTPUT
+                        Output bed file
+  -s SAMPLE, --sample SAMPLE
+                        Sample name in VCF file to use. Will default to first
+                        sample (alphabetically) if not supplied
+  -q QUALITY, --quality QUALITY
+                        Minimum genotype quality (default 20)
+  -nq NON_VARIANT_QUALITY, --non-variant-quality NON_VARIANT_QUALITY
+                        Minimum genotype quality for non-variant records
+                        (default 20)
+  -b, --bedgraph        Output in bedgraph mode
diff --git a/bin/pseudo_bam.sh b/bin/pseudo_bam.sh
@@ -22,7 +22,7 @@ function reheader(){
 				mv -v "${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<"${mapping}"
 fi
diff --git a/bin/tortilla.sh b/bin/tortilla.sh
@@ -33,33 +33,33 @@ fi
 if [[ "${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