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Does MuTect2 actually support GVCF output?

MuTect2 docs since 3.5-0 listed the possibility of GVCF output by using -ERC GVCF. However, it seems to me that for both 3.5-0 or 3.6-0 versions, adding that flag would still give out a standard VCF despite MuTect2 never gave any errors. The following is my most recent attempt in running a tumor-only under version 3.6-0:

INFO 14:28:51,867 HelpFormatter - ---------------------------------------------------------------------------------- INFO 14:28:51,873 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29 INFO 14:28:51,873 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 14:28:51,873 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk INFO 14:28:51,873 HelpFormatter - [Thu Aug 18 14:28:51 CDT 2016] Executing on Linux 2.6.32-431.23.3.el6.x86_64 amd64 INFO 14:28:51,874 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 JdkDeflater INFO 14:28:51,879 HelpFormatter - Program Args: -T MuTect2 -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 -ERC GVCF -R GRCm38.primary_assembly.genome.fa -I:tumor [redacted].bam -o [redacted].g.vcf -A DepthPerAlleleBySample -A BaseQualitySumPerAlleleBySample -A TandemRepeatAnnotator -A OxoGReadCounts -A StrandOddsRatio -A QualByDepth INFO 14:28:51,893 HelpFormatter - Executing as [redacted] on Linux 2.6.32-431.23.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14. INFO 14:28:51,894 HelpFormatter - Date/Time: 2016/08/18 14:28:51 INFO 14:28:51,894 HelpFormatter - ---------------------------------------------------------------------------------- INFO 14:28:51,894 HelpFormatter - ---------------------------------------------------------------------------------- INFO 14:28:51,919 GenomeAnalysisEngine - Strictness is SILENT INFO 14:28:52,060 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 14:28:52,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:28:52,173 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10 INFO 14:28:52,326 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 14:28:52,555 GenomeAnalysisEngine - Done preparing for traversal INFO 14:28:52,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 14:28:52,556 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 14:28:52,557 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 14:28:52,705 MuTect2 - Using global mismapping rate of 45 => -4.5 in log10 likelihood units Using un-vectorized C++ implementation of PairHMM INFO 14:28:57,754 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file INFO 14:28:57,755 VectorLoglessPairHMM - Using vectorized implementation of PairHMM INFO 14:29:22,561 ProgressMeter - chr1:9725025 0.0 30.0 s 49.6 w 0.4% 2.3 h 2.3 h [PROGRESS BAR SKIPPED] INFO 00:48:24,238 VectorLoglessPairHMM - Time spent in setup for JNI call : 15.572278883000001 INFO 00:48:24,240 PairHMM - Total compute time in PairHMM computeLikelihoods() : 23910.506618779 INFO 00:48:24,241 MuTect2 - Ran local assembly on 25716 active regions INFO 00:48:24,319 ProgressMeter - done 2.730871774E9 10.3 h 13.0 s 100.0% 10.3 h 0.0 s INFO 00:48:24,320 ProgressMeter - Total runtime 37171.76 secs, 619.53 min, 10.33 hours INFO 00:48:24,321 MicroScheduler - 234625349 reads were filtered out during the traversal out of approximately 289615342 total reads (81.01%) INFO 00:48:24,322 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter INFO 00:48:24,322 MicroScheduler - -> 144777505 reads (49.99% of total) failing DuplicateReadFilter INFO 00:48:24,323 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 00:48:24,324 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 00:48:24,325 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 00:48:24,325 MicroScheduler - -> 89847844 reads (31.02% of total) failing NotPrimaryAlignmentFilter INFO 00:48:24,326 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
The VCF is unremarkable, had it been a standard MuTect2 VCF.

Although, I personally think that due to the MuTect2 hard filters, it's probably not a good idea for it to output GVCF anyway.

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  • johnmajohnma Member

    This is just to reported that the behavior is the same when I use -ERC BP_RESOLUTION, i.e. MuTect2 outputting a standard VCF file.

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