#!/bin/env bash set -euo pipefail IFS=$'\n' /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx20g" \ FastqToSam \ --F1 ERR250256_1.filt.fastq.gz \ --F2 ERR250256_2.filt.fastq.gz \ --OUTPUT "ERR250256.bam" \ --SAMPLE_NAME test_sample \ --LIBRARY_NAME test_lib \ --PLATFORM illumina \ --PLATFORM_UNIT test_pu \ --READ_GROUP_NAME test_rg \ --COMPRESSION_LEVEL 1 \ --VALIDATION_STRINGENCY SILENT \ --SORT_ORDER queryname /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx4g" \ SamToFastq \ --COMPRESSION_LEVEL 5 \ --INPUT ERR250256.bam \ --FASTQ /dev/stdout \ --INTERLEAVE true \ --NON_PF true \ | \ /home/evaben/download/bwa-0.7.15/bwa mem -K 100000000 -v 3 -Y -t "16" -p Homo_sapiens_assembly38.fasta /dev/stdin \ | \ /home/evaben/download/samtools-1.8/samtools view -b -o ERR250256.unmerged.bam /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx5g" \ MergeBamAlignment \ --COMPRESSION_LEVEL 5 \ --VALIDATION_STRINGENCY SILENT \ --EXPECTED_ORIENTATIONS FR \ --ATTRIBUTES_TO_RETAIN X0 \ --ALIGNED_BAM ERR250256.unmerged.bam \ --UNMAPPED_BAM ERR250256.bam \ --OUTPUT ERR250256.aligned.unsorted.bam \ --REFERENCE_SEQUENCE Homo_sapiens_assembly38.fasta \ --PAIRED_RUN true \ --SORT_ORDER "unsorted" \ --IS_BISULFITE_SEQUENCE false \ --ALIGNED_READS_ONLY false \ --CLIP_ADAPTERS false \ --MAX_RECORDS_IN_RAM 2000000 \ --ADD_MATE_CIGAR true \ --MAX_INSERTIONS_OR_DELETIONS -1 \ --PRIMARY_ALIGNMENT_STRATEGY MostDistant \ --UNMAPPED_READ_STRATEGY COPY_TO_TAG \ --ALIGNER_PROPER_PAIR_FLAGS true \ --UNMAP_CONTAMINANT_READS true /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ MarkDuplicates \ --INPUT ERR250256.aligned.unsorted.bam \ --OUTPUT ERR250256.hg38.aligned.unsorted.duplicates_marked.bam \ --METRICS_FILE ERR250256.hg38.duplicate_metrics \ --COMPRESSION_LEVEL 5 \ --VALIDATION_STRINGENCY SILENT \ --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 \ --ASSUME_SORT_ORDER "queryname" \ --CREATE_MD5_FILE true /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g -XX:ParallelGCThreads=1" \ SortSam \ --INPUT ERR250256.hg38.aligned.unsorted.duplicates_marked.bam \ --OUTPUT /dev/stdout \ --COMPRESSION_LEVEL 5 \ --MAX_RECORDS_IN_RAM 2500000 \ --SORT_ORDER "coordinate" \ --CREATE_INDEX false \ --CREATE_MD5_FILE false \ | \ /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx4g -XX:ParallelGCThreads=1" \ SetNmAndUqTags \ --INPUT /dev/stdin \ --OUTPUT ERR250256.hg38.aligned.duplicate_marked.sorted.bam \ --COMPRESSION_LEVEL 5 \ --CREATE_INDEX true \ --CREATE_MD5_FILE true \ --REFERENCE_SEQUENCE Homo_sapiens_assembly38.fasta #bqsr /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ BaseRecalibrator \ -R Homo_sapiens_assembly38.fasta \ -I ERR250256.hg38.aligned.duplicate_marked.sorted.bam \ --use-original-qualities \ -O ERR250256.hg38.recal_data.scatter1.csv \ --known-sites Homo_sapiens_assembly38.dbsnp138.vcf \ --known-sites Homo_sapiens_assembly38.known_indels.vcf.gz \ -L chr1:1+ /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ BaseRecalibrator \ -R Homo_sapiens_assembly38.fasta \ -I ERR250256.hg38.aligned.duplicate_marked.sorted.bam \ --use-original-qualities \ -O ERR250256.hg38.recal_data.scatter2.csv \ --known-sites Homo_sapiens_assembly38.dbsnp138.vcf \ --known-sites Homo_sapiens_assembly38.known_indels.vcf.gz \ -L chr2:1+ /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ GatherBQSRReports \ -I ERR250256.hg38.recal_data.scatter1.csv \ -I ERR250256.hg38.recal_data.scatter2.csv \ -O ERR250256.hg38.recal_data.csv #apply /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ ApplyBQSR \ -R Homo_sapiens_assembly38.fasta \ -I ERR250256.hg38.aligned.duplicate_marked.sorted.bam \ -O ERR250256.hg38.scatter1.bam \ -L chr1:1+ \ -bqsr ERR250256.hg38.recal_data.csv \ --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \ --add-output-sam-program-record \ --create-output-bam-md5 \ --use-original-qualities /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ ApplyBQSR \ -R Homo_sapiens_assembly38.fasta \ -I ERR250256.hg38.aligned.duplicate_marked.sorted.bam \ -O ERR250256.hg38.scatter2.bam \ -L chr2:1+ \ -bqsr ERR250256.hg38.recal_data.csv \ --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \ --add-output-sam-program-record \ --create-output-bam-md5 \ --use-original-qualities /home/evaben/download/gatk-4.0.4.0/gatk --java-options "-Xmx10g" \ GatherBamFiles \ --INPUT ERR250256.hg38.scatter1.bam \ --INPUT ERR250256.hg38.scatter2.bam \ --OUTPUT ERR250256.hg38.bam \ --COMPRESSION_LEVEL 5 \ --CREATE_INDEX true \ --CREATE_MD5_FILE true