After BQSR, Why don't create a header ?
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When I run the BQSR with GATK 2.8.1, I can't check the PG information on output bam file.

BWA->Picard dedup->GATK LocalRealign->GATK BQSR

Below is the output BAM file after BQSR step.

@PG ID:GATK IndelRealigner VN:2.3-9-gdcdccbb CL:knownAlleles=[(RodBinding name=knownAlleles source=/nG/Reference/hgdownload.cse.ucsc.edu/goldenPath/hg19/KNOWNINDEL/Mills_and_1000G_gold_standard.indels.hg19.vcf)] targetIntervals=/nG/Data/2077/vcf1/node1/chrY/Databind/chrY.bam.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null @PG ID:MarkDuplicates PN:MarkDuplicates VN:1.92(1464) CL:net.sf.picard.sam.MarkDuplicates INPUT=[/nG/Data/2077/step2_makebam/node1-1.bam, /nG/Data/2077/step2_makebam/node1-2.bam, /nG/Data/2077/step2_makebam/node1-3.bam, /nG/Data/2077/step2_makebam/node1-4.bam, /nG/Data/2077/step2_makebam/node1-5.bam, /nG/Data/2077/step2_makebam/node1-6.bam] OUTPUT=/dev/stdout METRICS_FILE=/nG/Data/2077/temp/picard_info.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000000 TMP_DIR=[/nG/Data/2077/temp] QUIET=true VALIDATION_STRINGENCY=LENIENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=2000000 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO CREATE_INDEX=false CREATE_MD5_FILE=false

Related thread (guess) http://gatkforums.broadinstitute.org/discussion/2118/baserecalibration-prinread-don-t-create-a-header-and-don-t-obtain-oq-orignal-base-quality-in-bam


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