fix variant-calling

bioinform · Nov 6, 2019 · fe68cf3 · fe68cf3
1 parent 9277d84
commit fe68cf3
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Showing 3 changed files with 5 additions and 7 deletions.
diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -140,6 +140,7 @@ RUN cd /opt && tar -xzvf IDP-fusion_${IDPFUSION_VERSION}.tar.gz && rm -rf /opt/I
 
 RUN wget https://github.com/broadinstitute/gatk/releases/download/4.1.4.0/gatk-4.1.4.0.zip -O /opt/gatk-4.1.4.0.zip  && cd /opt && unzip gatk-4.1.4.0.zip && chmod -R 755 /opt/gatk-4.1.4.0
 
+ENV GATK_VERSION 4.1.4.0
 ENV GATK_VERSION 4.1.4.0
 
 RUN pip install https://github.com/bioinform/rnacocktail/archive/update_tools.zip

diff --git a/src/run_variant.py b/src/run_variant.py
@@ -162,7 +162,7 @@ def run_gatk(alignment="", ref_genome="", knownsites="",
         msg = "GATK BaseRecalibrator for %s"%sample
         if start<=step:
             logger.info("--------------------------STEP %s--------------------------"%step)
-            command="%s %s -jar %s BaseRecalibrator -R %s -I %s  -o %s/recal_data.table %s" % (
+            command="%s %s -jar %s BaseRecalibrator -R %s -I %s  -O %s/recal_data.table %s" % (
                 java, java_opts, gatk, ref_genome,split_bam,work_gatk,BaseRecalibrator_opts)
             command="bash -c \"%s\""%command      
             cmd = TimedExternalCmd(command, logger, raise_exception=True)
@@ -174,7 +174,7 @@ def run_gatk(alignment="", ref_genome="", knownsites="",
         msg = "GATK PrintReads for %s"%sample
         if start<=step:
             logger.info("--------------------------STEP %s--------------------------"%step)
-            command="%s %s -jar %s PrintReads -R %s -I %s -BQSR %s/recal_data.table -o %s/bsqr.bam %s" % (
+            command="%s %s -jar %s PrintReads -R %s -I %s -BQSR %s/recal_data.table -O %s/bsqr.bam %s" % (
                 java, java_opts, gatk, ref_genome,split_bam,work_gatk,work_gatk,PrintReads_opts)
             command="bash -c \"%s\""%command      
             cmd = TimedExternalCmd(command, logger, raise_exception=True)
@@ -194,7 +194,7 @@ def run_gatk(alignment="", ref_genome="", knownsites="",
     msg = "GATK HaplotypeCaller for %s"%sample
     if start<=step:
         logger.info("--------------------------STEP %s--------------------------"%step)
-        command="%s %s -jar %s HaplotypeCaller -R %s -I %s -o %s/variants.vcf %s" % (
+        command="%s %s -jar %s HaplotypeCaller -R %s -I %s -O %s/variants.vcf %s" % (
             java, java_opts, gatk, ref_genome,split_bam,work_gatk,HaplotypeCaller_opts)
         command="bash -c \"%s\""%command      
         cmd = TimedExternalCmd(command, logger, raise_exception=True)
@@ -206,7 +206,7 @@ def run_gatk(alignment="", ref_genome="", knownsites="",
     msg = "GATK VariantFiltration for %s"%sample
     if start<=step:
         logger.info("--------------------------STEP %s--------------------------"%step)
-        command="%s %s -jar %s VariantFiltration -R %s -V %s/variants.vcf -o %s/variants_filtered.vcf %s" % (
+        command="%s %s -jar %s VariantFiltration -R %s -V %s/variants.vcf -O %s/variants_filtered.vcf %s" % (
             java, java_opts, gatk, ref_genome,work_gatk,work_gatk,VariantFiltration_opts)
         command="bash -c \"%s\""%command      
         cmd = TimedExternalCmd(command, logger, raise_exception=True)

diff --git a/test/docker_test.sh b/test/docker_test.sh
@@ -329,7 +329,6 @@ docker run -u $UID -v=${PWD}/../:/work_dir/ rnacocktail:0.3 run_rnacocktail.py v
 				--threads 10 \
 				--sample E \
 				--ref_genome /work_dir/example/GRCh38_full_analysis_set_plus_decoy_hla.fa \
-				--IndelRealignment \
 				--CleanSam \
 				--knownsites /work_dir/example/All_20180418.vcf \
 				--picard /usr/local/bin/picard.jar
@@ -382,7 +381,6 @@ docker run -u $UID -v=${PWD}/../:/work_dir/ rnacocktail:0.3 run_rnacocktail.py a
 				--quantifier_idx /work_dir/example/Homo_sapiens.GRCh38.cdna.21.Salmon.fmd \
 				--unzip \
 				--file_format fastq.gz \
-				--IndelRealignment \
 				--CleanSam \
 				--knownsites /work_dir/example/variants_21.vcf \
 				--strand_pos /work_dir/example/GRCh38_strand_pos_.bed \
@@ -429,7 +427,6 @@ docker run -u $UID -v=${PWD}/../:/work_dir/ rnacocktail:0.3 run_rnacocktail.py a
 				--ref_all_gpd /work_dir/example/GRCh38.21.gpd \
 				--ref_gpd /work_dir/example/refFlat.21.txt \
 				--file_format fasta \
-				--IndelRealignment \
 				--CleanSam \
 				--knownsites /work_dir/example/variants_21.vcf \
 				--strand_pos /work_dir/example/GRCh38_strand_pos_.bed \