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[admin]

http://bio-bwa.sourceforge.net/bwa.shtml

程式碼: [Select]

bwa index ref.fa

bwa mem ref.fa reads.fq > aln-se.sam

bwa mem ref.fa read1.fq read2.fq > aln-pe.sam

bwa aln ref.fa short_read.fq > aln_sa.sai

bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam

bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam

bwa bwasw ref.fa long_read.fq > aln.sam

[ngstool]

程式碼: [Select]

samtools view -b -S SLE001-bwa.sam > SLE001-bwa.bam
samtools sort SLE001-bwa.bam SLE001-bwa-sorted
samtools index  SLE001-bwa-sorted.bam
java -jar picard.jar MarkDuplicates INPUT=SLE001-bwa-sorted.bam OUTPUT=SLE001-bwa-dedup.bam METRICS_FILE=metrics.txt