RRedon:Protocols/Variation pipeline/MAQ


 * 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
 * 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

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