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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KARMA is obsolete and not maintained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
# Some instructions for read mapping and variant calling using the
# University of Michigan tools and procedures.
# University of Michigan tools and procedures.
# -- Paul Anderson and Tom Blackwell, December 11, 2009 --
# -- Paul Anderson and Tom Blackwell, December 11, 2009 --
# software components of this process are:
# software components of this process are:
# bwa index # Do this only when a new version of the genome reference
# 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
# 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
# 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)
# 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.
# Sample command lines. This is csh syntax.
-t ../bwa.ref/human_g1k_v37.fasta.fai \
-t ../bwa.ref/human_g1k_v37.fasta.fai \
-g - > person.glf
-g - > person.glf
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