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| + | <!-- BANNER ACROSS TOP OF PAGE --> |
| + | {| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" | |
| + | | style="width:100%; text-align:center; white-space:nowrap; color:#000;" | |
| + | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">KARMA is obsolete and not maintained</div> |
| + | |} |
| + | |
| + | <source lang="text"> |
| + | |
| # 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 -- |
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| # 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.
| + | # 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
| + | # variable timings -- takes between 10 minutes and many |
− | # hours per .fastq file. Better data runs quicker.
| + | # 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.
| + | # 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.
| + | # to a single .sam alignment file. 1 - 2 minutes per run. |
− | # (In general, the CEU trio chromosome 20 test data set
| + | # (In general, the CEU trio chromosome 20 test data set |
− | # contains VERY small .fastq files. Chromosome 20 is just
| + | # contains VERY small .fastq files. Chromosome 20 is just |
− | # over 2% of the entire genome.)
| + | # over 2% of the entire genome.) |
| | | |
| # Sample command lines. This is csh syntax. | | # Sample command lines. This is csh syntax. |
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| -t ../bwa.ref/human_g1k_v37.fasta.fai \ | | -t ../bwa.ref/human_g1k_v37.fasta.fai \ |
| -g - > person.glf | | -g - > person.glf |
| + | |
| + | </source> |