RRedon:Protocols/Variation pipeline/BWA: Difference between revisions
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* Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. | * Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. | ||
bwa sampe hg18.fasta output1.aln output2.aln file1.fastq.gz file2.fastq.gz | gzip --best > output.sam | bwa sampe hg18.fasta output1.aln output2.aln file1.fastq.gz file2.fastq.gz | gzip --best > output.sam.gz | ||
Latest revision as of 00:49, 9 June 2010
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Indexing the reference sequence
See Main article : Reference genome
Map
- Align one fastq files
-l Take the first INT subsequence as seed
-q Parameter for read trimming.
-t number of threads = 10 on server 2
bwa aln -l 32 -q 15 -t 10 -foutput1.aln hg18.fasta file1.fastq.gz bwa aln -l 32 -q 15 -t 10 -foutput2.aln hg18.fasta file2.fastq.gz
- Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
bwa sampe hg18.fasta output1.aln output2.aln file1.fastq.gz file2.fastq.gz | gzip --best > output.sam.gz
- export to bam ?
samtools view output.sam > output.bam
← Fix this! I used this ?
Use the reference genome indexed by samtools
samtools import hg18.fa.fai output.sam output.bam samtools sort output.bam output.bam.sorted samtools index chr1.sorted.bam
- sort bam
samtools sort output.bam sorted_prefix
do insert size stats e.g. 99.8 percentile for MAQ max insert size ← Fix this! what does that mean ?
