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, 02:42, 17 February 2010
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| | Michigan Pilot One SNP calling work flow: | | Michigan Pilot One SNP calling work flow: |
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| − | (1) Create GLF files from BAM files
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| − | (2) Split GLF files by chromosome
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| − | (3) Build a list of individuals within each population
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| − | (4) Link files and tabulate # of files per population, per platform
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| − | (5) Check total depth for each population, each platform
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| − | (6) Filter sites with total depth at the extremes, within each population, each platform
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| − | (7) Obtain one merged GLF for each individual by merging GLFs across platforms for the same individual
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| − | (8) Promote a set of sites for each population
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| − | (9) Merge with genotype data
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| − | (10) Run thunder
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| − | (11) Ligate thunder results for larger chromosomes
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| − | (12) Extract QC+ sites
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| − | (13) Generate other information for VCF format
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| − | (14) Generate VCF
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| − | (15) Quality check
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| − | <br>
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| | == (1) Create GLF files from BAM files == | | == (1) Create GLF files from BAM files == |
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| | Parameters:<br> minMapQ = 30 | | Parameters:<br> minMapQ = 30 |
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| − | back<br> <br>(7) Obtain one merged GLF for each individual by merging GLFs across platforms for the same individual
| + | == (7) Obtain one merged GLF for each individual by merging GLFs across platforms for the same individual == |
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| | /home/ylwtx/codes/cpp/mach-1.0.16/test_thunder/2009.09.all/ | | /home/ylwtx/codes/cpp/mach-1.0.16/test_thunder/2009.09.all/ |
