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Examples of Read Mapping with Karma and BWA

493 bytes added, 15:50, 23 September 2014
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">KARMA is obsolete and not maintained</div>
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# Some instructions for read mapping and variant calling using the
# University of Michigan tools and procedures.
# -- Paul Anderson and Tom Blackwell, December 11, 2009 --
# software components of this process are:
# bwa index # -- Do this only when a new version of the genome reference # sequence is released. Takes just under two hours. # bwa aln # -- Run this on every .fastq file individually. Highly # variable timings -- takes between 10 minutes and many # hours per .fastq file. Better data runs quicker. # bwa samse # -- Converts a single .fastq / .sai pair to .sam alignment # format. Usually under 1 minute per file. # bwa sampe # -- Converts paired end .fastq / .sai pairs (four files total) # to a single .sam alignment file. 1 - 2 minutes per run. # (In general, the CEU trio chromosome 20 test data set # contains VERY small .fastq files. Chromosome 20 is just # over 2% of the entire genome.)
# Sample command lines. This is csh syntax.
-t ../bwa.ref/human_g1k_v37.fasta.fai \
-g - > person.glf
 
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