RRedon:Protocols/Variation pipeline/MAQ: Difference between revisions
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* [http://maq.sourceforge.net/ http://maq.sourceforge.net/] | * [http://maq.sourceforge.net/ http://maq.sourceforge.net/] | ||
=Indexing the Reference Sequence= | |||
See Main article : [[RRedon:Protocols/Variation_pipeline/Reference_genome#MAQ|Reference genome]] | |||
==Pre-Mapping== | |||
* split fastq files in to chunks of 1 million PE reads {{fix-this|why?}} | * split fastq files in to chunks of 1 million PE reads {{fix-this|why?}} | ||
** foreach fastq file : | ** foreach fastq file : | ||
Latest revision as of 08:23, 2 June 2010
Indexing the Reference Sequence
See Main article : Reference genome
Pre-Mapping
- split fastq files in to chunks of 1 million PE reads ← Fix this! why?
- foreach fastq file :
maq fastq2bfq $fq $bfq maq map -e 70 -a max_insert_size_for_lane -u $unmapped $mapped $bfa $bfq_1 $bfq_2
custom convert $unmapped > $unmapped.sam
samtools view $unmapped.sam > $unmapped.bam samtools view $mapped > $mapped.bam
← Fix this! what shall we do with unmapped ? look for indels ?
merge @bam using picardtools v1.08 MergeSamFiles.jar > $final.bam
samtools sort -n $final.bam $final.nameSort samtools fixmate $final.nameSort.bam $final.fm.bam samtools sort $final.fm.bam $final.fm_coordSort
