v2.5

patidarr · Feb 3, 2017 · c749405 · c749405
1 parent aa54a53
commit c749405
Show file tree

Hide file tree

Showing 4 changed files with 11 additions and 10 deletions.
diff --git a/config/config_common.json b/config/config_common.json
@@ -1,7 +1,7 @@
 {
-	"pipeline_version"	: "v2.4",
-	"mail"			: "-c patidarr@mail.nih.gov",
-	"mails"			: "-c patidarr@mail.nih.gov -c weij@mail.nih.gov -c manoj.tyagi@nih.gov -c khanjav@mail.nih.gov -c wangc@mail.nih.gov -c yujin.lee@nih.gov",
+	"pipeline_version"	: "v2.5",
+	"mails"			: "-c patidarr@mail.nih.gov",
+	"mail"			: "-c patidarr@mail.nih.gov -c weij@mail.nih.gov -c manoj.tyagi@nih.gov -c khanjav@mail.nih.gov -c wangc@mail.nih.gov -c yujin.lee@nih.gov",
 	"platform"		: "Illumina",
 	"samtools"		: "0.1.19",
 	"samtools_old"		: "0.1.19",

diff --git a/ngs_pipeline.snakefile b/ngs_pipeline.snakefile
@@ -128,7 +128,7 @@ for subject  in config['RNASeq'].keys():
 ALL_FASTQC  = ["{subject}/{TIME}/{sample}/qc/fastqc/{sample}_R2_fastqc.html".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC      = ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.flagstat.txt".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC     += ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.squeeze.done".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
-#ALL_QC     += ["{subject}/{TIME}/{sample}/verifyBamID/{sample}.selfSM".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
+ALL_QC     += ["{subject}/{TIME}/{sample}/verifyBamID/{sample}.selfSM".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC     += ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.hotspot.depth".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC     += ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.gt".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 #ALL_QC     += ["{subject}/{TIME}/{sample}/qc/BamQC/qualimapReport.html".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
@@ -246,7 +246,7 @@ for sample in config['sample_references'].keys():
 	if config['sample_captures'][sample] not in config['Panel_List']:
 		COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/sequenza/"+sample+"/"+sample+"_alternative_fit.pdf"]
 		COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/sequenza/"+sample+".txt"]
-		COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/NeoAntigen/MHC_Class_I/"+sample+".final.tsv"]
+		#COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/NeoAntigen/MHC_Class_I/"+sample+".final.tsv"]
 	SOMATIC     +=[subject+"/"+TIME+"/"+sample+"/calls/"+sample+".MuTect.annotated.txt"]
 	SOMATIC     +=[subject+"/"+TIME+"/"+sample+"/calls/"+sample+".strelka.snvs.annotated.txt"]
 	SOMATIC     +=[subject+"/"+TIME+"/"+sample+"/calls/"+sample+".strelka.indels.annotated.txt"]

diff --git a/ruleBook/readDepth.snakefile b/ruleBook/readDepth.snakefile
@@ -12,12 +12,13 @@ rule ReadDepth:
 	params:
 		rulename	= "readDepth",
 		R 		= config['version_R'],
+		samtools	= config['samtools'],
 		batch		= config[config['host']]["job_bedtools"]
 	shell: """
 	#######################	
-	module load bedtools/{version}
-	module load R/{params.R}
+	module load bedtools/{version} samtools/{params.samtools}
 	echo -e "chr\\tstart\\tend\\tgene\\tposition\\tdepth" >  {output}
-	cut -f1-4 {input.target_intervals} | bedtools coverage -abam {input.bam} -b - -d >> {output}
+	samtools view -hF 0x400 -q 30 -L {input.target_intervals} {input.bam} | samtools view -ShF 0x4 - | samtools view -SuF 0x200 - | bedtools coverage -abam - -b {input.target_intervals} -d >> {output}
+	#cut -f1-4 {input.target_intervals} | bedtools coverage -abam {input.bam} -b - -d >> {output}
 	#######################
 	"""
diff --git a/submit_snakemake.sh b/submit_snakemake.sh
@@ -59,8 +59,8 @@ fi
 export ACT_DIR="/Actionable/"
 SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.snakefile
 
-cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R RNASeq "
-#cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R makeConfig RNASeq "
+#cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R RNASeq "
+cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R makeConfig RNASeq "
 umask 022
 if [ $HOST   == 'biowulf.nih.gov' ]; then
 	echo "Host identified as $HOST"