BWA使用及参数讲解.pptx

BWA 使用及参数讲解 李延红 2011-09-20 CONTENTS Description Synopsis Commands and Options 2 Description BWA is a fast alignment tool. Two different algorithms, both based on BWT. The first is designed for short sequencing reads(=200bp),the second is for long reads. 3 Synopsis bwa index -a bwtsw database.fasta bwa aln database.fasta short_read.fastq aln_sa.sai bwa samse database.fasta aln_sa.sai short_read.fastq aln.sam bwa sampe database.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq aln.sam bwa bwasw database.fasta long_read.fastq aln.sam 4 Commands And Options Index Index database sequences in the fasta format. bwa index [-a algoType] in.db.fasta -a is database smaller than or equal 2GB bwtsw database larger than or equal 10MB 5 Commands And Options aln Find the SA coordinates of the input reads. bwa aln [options] in.db.fasta in.query.fq out.sai 6 Commands And Options Options: -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04] -o INT maximum number or fraction of gap opens [1] -e INT maximum number of gap extensions, -1 for disabling long gaps [-1] -i INT do not put an indel within INT bp towards the ends [5] -d INT maximum occurrences for extending a long deletion [10] -l INT seed length [32] -k INT maximum differences in the seed [2] -t INT number of threads [1] -q INT quality threshold for read trimming down to 35bp [0] -f FILE file to write output to instead of stdout -L log-scaled gap penalty for long deletions -I the input is in the Illumina 1.3+ FASTQ-like format 7 Commands And Options Samse Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen. bwa samse in.db.fasta in.sai in.fq out.sam 8 Commands And Options sampe Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randoml