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java -jar <path to GenomeAnalysisTK.jar> -T CountReads -R AP012030-new.fasta -I Kishimoto_01_43B_S1.bam
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gatk CountReads -R AP012030-new.fasta -I Kishimoto_01_43B_S1.bam
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How can I prepare a FASTA file to use as reference? — GATK-Forum
dict
java -jar CreateSequenceDictionary.jar R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict
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gatk CreateSequenceDictionary -R AP012030-new.fasta -O AP012030-new.dict
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samtools faidx AP012030-new.fasta
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$ gatk CountReads -R AP012030-new.fasta -I Kishimoto_01_43B_S1.bam Using GATK jar /usr/local/src/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true \ -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 \ -jar /usr/local/src/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar CountReads \ -R AP012030-new.fasta -I Kishimoto_01_43B_S1.bam 15:39:33.994 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/src/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 15:39:36.370 INFO CountReads - ------------------------------------------------------------ 15:39:36.372 INFO CountReads - The Genome Analysis Toolkit (GATK) v4.1.2.0 15:39:36.373 INFO CountReads - For support and documentation go to https://software.broadinstitute.org/gatk/ 15:39:36.375 INFO CountReads - Executing as yamanouc@pepper.is.sci.toho-u.ac.jp on Linux v3.10.0-514.2.2.el7.x86_64 amd64 15:39:36.376 INFO CountReads - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_111-b15 15:39:36.377 INFO CountReads - Start Date/Time: 2019/05/16 15:39:33 JST 15:39:36.378 INFO CountReads - ------------------------------------------------------------ 15:39:36.378 INFO CountReads - ------------------------------------------------------------ 15:39:36.380 INFO CountReads - HTSJDK Version: 2.19.0 15:39:36.380 INFO CountReads - Picard Version: 2.19.0 15:39:36.380 INFO CountReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2 15:39:36.381 INFO CountReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 15:39:36.381 INFO CountReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 15:39:36.381 INFO CountReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 15:39:36.382 INFO CountReads - Deflater: IntelDeflater 15:39:36.382 INFO CountReads - Inflater: IntelInflater 15:39:36.383 INFO CountReads - GCS max retries/reopens: 20 15:39:36.383 INFO CountReads - Requester pays: disabled 15:39:36.383 INFO CountReads - Initializing engine 15:39:39.020 INFO CountReads - Done initializing engine 15:39:39.021 INFO ProgressMeter - Starting traversal 15:39:39.021 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 15:56:29.987 INFO CountReads - 60820166 read(s) filtered by: WellformedReadFilter 15:56:29.997 INFO ProgressMeter - unmapped 16.8 0 0.0 15:56:29.997 INFO ProgressMeter - Traversal complete. Processed 0 total reads in 16.8 minutes. 15:56:29.998 INFO CountReads - Shutting down engine [2019/05/16 15:56:29 JST] org.broadinstitute.hellbender.tools.CountReads done. Elapsed time: 16.94 minutes. Runtime.totalMemory()=4494721024
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Performance benchmarking of GATK3.8 and GATK4
$gatk MarkDuplicates -I Kishimoto_01_43B_S1.sorted.bam \ -M Kishimoto_01_43B_S1.duplicated.metrics -O Kishimoto_01_43B_S1.dedup.sorted.bam --ASSUME_SORTED TRUE --REMOVE_DUPLICATES TRUE