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I find that I always lose all the variants on mitochondria with sensitive tranche 99%. And all the variants on mitochondria fall in the FILTER flag "VQSRTrancheSNP99.90to100.00". Then I check the reference used by VQSR. Among HapMap, 1KG,…
Hello, I saw there is 1000G phase 3 VCF data in bundle already. Is it better to replace phase 1 VCF file with phase 3 VCF file in VQSR? Can I just use this new version file within the old command?
I am in front of a similar problem with WGS DNA data(Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29). After CombineGVCFs or GenotypeGVCFs, output VCF always includes “” ATL of some sites. While gVCF files do not contain…
Thanks for @Sheila 's reply. I also checked more implement of RealignerTargetCreator these days, and confirmed there is no error in the final bam output. But I do hope GATK will correct this misleading log info in the near future.
I got a confusing log after I set "-nt" parameter to 24 when I use RealignerTargetCreator(GATK v3.2-0-g289df4b): .... INFO 16:45:20,577 MicroScheduler - Running the GATK in parallel mode with 24 total threads, 1 CPU thread(s) for each of…