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Old 01-03-2016, 03:15 PM   #1
Mike_Brown
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Default missing the read group (RG) tag, which is required by the GATK.

I am new to GATK and BAM file. I want to convert bam file into vcf file by running
Code:
java -jar /media/zwang10/Elements/UK10K/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -T HaplotypeCaller -I _EGAR00001038931_36843.pe.raw.sorted.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o raw_variants.vcf
But I got
Code:
INFO  19:14:00,776 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  19:14:00,783 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
INFO  19:14:00,784 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  19:14:00,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  19:14:00,793 HelpFormatter - Program Args: -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -T HaplotypeCaller -I _EGAR00001038931_36843.pe.raw.sorted.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o raw_variants.vcf 
INFO  19:14:00,806 HelpFormatter - Executing as zwang10@zwang10-K55N on Linux 3.13.0-74-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02. 
INFO  19:14:00,807 HelpFormatter - Date/Time: 2016/01/03 19:14:00 
INFO  19:14:00,808 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  19:14:00,808 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  19:14:01,199 GenomeAnalysisEngine - Strictness is SILENT 
INFO  19:14:01,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500 
INFO  19:14:01,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  19:14:01,668 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15 
INFO  19:14:01,739 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 
INFO  19:14:01,982 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  19:14:03,265 GenomeAnalysisEngine - Done preparing for traversal 
INFO  19:14:03,266 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  19:14:03,268 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining 
INFO  19:14:03,269 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime 
INFO  19:14:03,270 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output 
INFO  19:14:03,390 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
WARN  19:14:03,391 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples. 
INFO  19:14:03,393 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
INFO  19:14:03,675 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units 
INFO  19:14:08,680 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.5-0-g36282e4): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@5c0bb1d5 is malformed. Please see http://gatkforums.broadinstitute.org/discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cramfor more information. Error details: Read FCC03A6ABXX:3:2107:11142:198335#TAGCTTAT is missing the read group (RG) tag, which is required by the GATK. Please see http://gatkforums.broadinstitute.org/discussion/59/companion-utilities-replacereadgroups to fix this problem
##### ERROR ------------------------------------------------------------------------------------------
Why does this bam file miss RG tag?
Can some one tell me how to add read group tag to
Code:
Read FCC03A6ABXX:3:2107:11142:198335#TAGCTTAT
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Old 01-03-2016, 04:21 PM   #2
GenoMax
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Similar question covered in this thread: http://seqanswers.com/forums/showthread.php?t=65293
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Old 01-04-2016, 12:34 PM   #3
vdauwera
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This is addressed in the GATK documentation:

https://www.broadinstitute.org/gatk/guide/article?id=59

Feel free to ask any other GATK-related questions in the GATK forum; we're there to help.
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