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, 11:11, 2 February 2017
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| + | {| style="width:100%; background:#FF8989; 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;">This tool has been DEPRECATED, and replaced by [[VerifyBamID]]</div> |
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| '''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals). | | '''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals). |
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| + | == Download bamGenotypeCheck == |
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| + | To get a copy go to the [http://csg.sph.umich.edu//pha/karma/download/ Karma Download] download page. |
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| + | == Build bamGenotypeCheck == |
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| + | Karma (which includes bamGenotypeCheck) is designed to be reasonably portable. |
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| + | However, since development occurs only on Ubuntu 9.10 x86 and x64 platforms, and later, there are likely other portability issues. |
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| + | We support Karma only on Ubuntu 9.10 and later on 64-bit processors. |
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| == Usage == | | == Usage == |
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| === Input Files === | | === Input Files === |
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− | -r ''genome reference in [[http://en.wikipedia.org/wiki/Fasta_format|simplified FASTA format]]'' | + | -r ''genome reference in [http://en.wikipedia.org/wiki/Fasta_format simplified FASTA format]'' |
| -a ''allele Frequency file in [[MERLIN format]]'' | | -a ''allele Frequency file in [[MERLIN format]]'' |
| -p ''pedigree file in [[MERLIN format]]'' | | -p ''pedigree file in [[MERLIN format]]'' |