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min_mapping_quality_score set up

Dear Sirs,

I have a bowtie2 alignment file which has many low mapping_quality reads (MPQ = 0).
I try to set up -mmq as 0. But it is not workable. Could you give me some suggestions?

The running message lists as follows:

INFO 17:26:46,957 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:26:46,960 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
INFO 17:26:46,961 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:26:46,961 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 17:26:46,968 HelpFormatter - Program Args: -T HaplotypeCaller -R reference.fa -I 20151117/GATK/27R-W0-sort-RG.bam -mmq 0 -stand_call_conf 30 -stand_emit_conf 10 -o Test-GATK.vcf
INFO 17:26:46,973 HelpFormatter - Executing as [email protected] on Linux 3.8.0-44-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_80-b15.
INFO 17:26:46,973 HelpFormatter - Date/Time: 2015/11/23 17:26:46
INFO 17:26:46,974 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:26:46,975 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:26:47,928 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:26:48,090 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 17:26:48,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:26:48,139 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
INFO 17:26:48,284 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 17:26:48,302 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:26:48,303 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:26:48,305 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:26:48,306 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 17:26:48,307 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output
INFO 17:26:48,536 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 17:26:48,537 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 17:26:48,550 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
WARN 17:26:54,658 PairHMMLikelihoodCalculationEngine$1 - Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING
INFO 17:26:54,659 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
INFO 17:26:54,659 HaplotypeCaller - Ran local assembly on 0 active regions
INFO 17:26:54,666 ProgressMeter - done 587.0 6.0 s 3.0 h 99.8% 6.0 s 0.0 s
INFO 17:26:54,667 ProgressMeter - Total runtime 6.36 secs, 0.11 min, 0.00 hours
INFO 17:26:54,668 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 43124 total reads (0.00%)
INFO 17:26:54,669 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 17:26:54,671 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 17:26:54,672 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 17:26:54,673 MicroScheduler - -> 0 reads (0.00% of total) failing HCMappingQualityFilter
INFO 17:26:54,673 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 17:26:54,674 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 17:26:54,675 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 17:26:54,676 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 17:26:57,275 GATKRunReport - Uploaded run statistics report to AWS S3

Answers

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