Difference between revisions of "Bwa"
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| + | As with samtools, bwa also went through some re-structuring, so that it has an old-style tw-step ('''aln''' and '''sam{s,p}e''') usage, characterised by the following typical sequence of commands: | ||
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| + | bwa index reference.fa | ||
| + | bwa aln -I -t 8 reference.fa s_1.txt > out.sai | ||
| + | bwa samse reference.fa out.sai s_1.txt > out.sam | ||
| + | samtools view -bSu out.sam | samtools sort - out.sorted | ||
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| + | And then a more modern usage which consists of just one step: '''bwa mem'''. | ||
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== Indexing == | == Indexing == | ||
When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name. | When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name. | ||
Revision as of 15:12, 30 November 2016
Introduction
Heng Li's aligner.
Usage
As with samtools, bwa also went through some re-structuring, so that it has an old-style tw-step (aln and sam{s,p}e) usage, characterised by the following typical sequence of commands:
bwa index reference.fa bwa aln -I -t 8 reference.fa s_1.txt > out.sai bwa samse reference.fa out.sai s_1.txt > out.sam samtools view -bSu out.sam | samtools sort - out.sorted
And then a more modern usage which consists of just one step: bwa mem.
Indexing
When bwa indexes a reference, it will use the whole filename and generate output index files with extensions added onto this name.
