RRedon:Protocols/Variation pipeline/MAQ

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• http://maq.sourceforge.net/

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