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align_bwa_illumina.sh 20202021_06_1405 Align Illumina SE or PE data with bwa. Produces a sorted, indexed, duplicate-marked BAM file and various statistics files. Usage: align_bwa_illumina.sh <aln_mode> <in_file> <out_pfx> <assembly> [ paired trim_sz trim_sz2 seq_fmt qual_fmt ] Required arguments: aln_mode Alignment mode, either global (bwa aln) or local (bwa mem). in_file For single-end alignments, path to input sequence file. For paired-end alignments using fastq, path to the the R1 fastq file which must contain the string 'R1' in its name. The corresponding 'R2' must have the same path except for 'R1'. out_pfx Desired prefix of output files in the current directory. assembly One of hg38, hg19, hg38, mm10, mm9, sacCer3, sacCer1, ce11, ce10, danRer7, hs_mirbase, mm_mirbase, or reference index prefix. Optional arguments: paired 0 = single end alignment (default); 1 = paired end. trim_sz Size to trim reads to. Default 0 (no trimming) trim_sz2 Size to trim R2 reads to for paired end alignments. Defaults to trim_sz seq_fmt Format of sequence file (fastq, bam or scarf). Default is fastq if the input file has a '.fastq' extension; scarf if it has a '.sequence.txt' extension. qual_type Type of read quality scores (sanger, illumina or solexa). Default is sanger for fastq, illumina for scarf. Environment variables: show_only 1 = only show what would be done (default not set) aln_args other bowtie2 options (e.g. '-T 20' for mem, '-l 20' for aln) no_markdup 1 = don't mark duplicates (default 0, mark duplicates) run_fastqc 1 = run fastqc (default 0, don't run). Note that output will be in the directory containing the fastq files. keep 1 = keep unsorted BAM (default 0, don't keep) bwa_bin BWA binary to use. Default bwa 0.7.x. Note that bwa 0.6.2 or earlier should be used for scarf and other short reads. also: NUM_THREADS, BAM_SORT_MEM, SORT_THREADS, JAVA_MEM_ARG Examples: align_bwa_illumina.sh local ABC_L001_R1.fastq.gz my_abc hg38 1 align_bwa_illumina.sh global ABC_L001_R1.fastq.gz my_abc hg38 1 50 align_bwa_illumina.sh global sequence.txt old sacCer3 0 '' '' scarf solexa |
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