updates from dnanexus

alignment/bamqc.sh

@@ -75,7 +75,7 @@ if [[ $nuctype == 'dna' ]]; then
 	#samtools view  -@ $threads ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
     fi
     #java -Xmx64g -Djava.io.tmpdir=${tmpdir} -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt TMP_DIR=${tmpdir}
-    if [[ $index_path/reference_info.pl ]]
+    if [[ $index_path/reference_info.txt ]]
     then
 	perl $baseDir/sequenceqc_dna.pl -e ${version} -r $index_path ${pair_id}.genomecov.txt
     else

variants/gatkrunner.sh

@@ -62,27 +62,6 @@ module load gatk/4.1.4.0 samtools/gcc/1.8
 which samtools
 samtools index -@ $NPROC ${sbam}
 
-if [[ $algo == 'gatkbam_rna' ]]
-then
-    module load picard/2.10.3
-    java -Xmx4g -jar $PICARD/picard.jar CleanSam INPUT=${sbam} OUTPUT=${pair_id}.clean.bam
-    java -Xmx4g -jar $PICARD/picard.jar ReorderSam I=${pair_id}.clean.bam O=${pair_id}.sort.bam R=${reffa} CREATE_INDEX=TRUE 
-    java -Xmx4g -jar $PICARD/picard.jar AddOrReplaceReadGroups INPUT=${pair_id}.clean.bam O=${pair_id}.rg_added_sorted.bam SO=coordinate RGID=${pair_id} RGLB=tx RGPL=illumina RGPU=barcode RGSM=${pair_id}
-    samtools index -@ $NPROC ${pair_id}.rg_added_sorted.bam
-    gatk SplitNCigarReads -R ${reffa} -I ${pair_id}.rg_added_sorted.bam -O ${pair_id}.split.bam
-    gatk --java-options "-Xmx32g" BaseRecalibrator -I ${pair_id}.split.bam --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
-    gatk --java-options "-Xmx32g" ApplyBQSR -I ${pair_id}.split.bam -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
-    samtools index -@ $NPROC ${pair_id}.final.bam
-elif [[ $algo == 'gatkbam' ]]
-then
-    gatk --java-options "-Xmx32g" BaseRecalibrator -I ${sbam} --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
-    gatk --java-options "-Xmx32g" ApplyBQSR -I ${sbam} -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
-    samtools index -@ $NPROC ${pair_id}.final.bam
-
-elif [[ $algo == 'abra2' ]]
-then
-  module load abra2/2.18
-  mkdir tmpdir
-  java  -Xmx16G -jar /cm/shared/apps/abra2/lib/abra2.jar --in ${sbam}  --in-vcf /archive/PHG/PHG_Clinical/phg_workflow/analysis/awesomeproject/GoldIndels.vcf --out ${pair_id}.final.bam --ref ${reffa} --threads $NPROC --tmpdir tmpdir
-  samtools index -@ $NPROC ${pair_id}.final.bam
-fi
+gatk --java-options "-Xmx32g" BaseRecalibrator -I ${sbam} --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
+gatk --java-options "-Xmx32g" ApplyBQSR -I ${sbam} -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
+samtools index -@ $NPROC ${pair_id}.final.bam

variants/somatic_vc.sh

@@ -94,6 +94,15 @@ then
 else
     interval=`cat ${reffa}.fai |cut -f 1 |grep -v decoy |grep -v 'HLA' |grep -v alt |grep -v 'chrUn' |grep -v 'random' | perl -pe 's/\n/ -L /g' |perl -pe 's/-L $//'`
 fi
+if [[ -z $tid ]]
+then
+    tid=`samtools view -H ${tumor} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+fi
+if [[ -z $nid ]]
+then
+    nid=`samtools view -H ${normal} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+fi
+
 
 source /etc/profile.d/modules.sh
 module load htslib/gcc/1.8