Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/README @ 6:361d6506850a
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author | ryanmorin |
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date | Tue, 18 Oct 2011 18:32:07 -0400 |
parents | 74f5ea818cea |
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5:a4975ec34575 | 6:361d6506850a |
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1 Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files | 1 Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files |
2 | 2 |
3 Installation | 3 Installation |
4 ------------ | 4 ------------ |
5 | 5 |
6 1) Place these files in $GALAXY_HOME/tools | 6 1) Place these files in $GALAXY_HOME/tools and compile/install SNVMix2 if you haven't already done so (also copy/link the SNVMix2 binary, |
7 2) Modify your configuration files appropriately, for example, add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section) | 7 identify_nonsynonymous_mutations.pl and filter_snvmix.pl to /usr/local/bin or some other location in the default PATH, also ensure they are executable) |
8 2) Modify your configuration files appropriately | |
9 -add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section), see the tool_conf.xml.sample for an example | |
10 -create or modify $GALAXY_HOME/sam_fa_indices.loc to match the example provided (points galaxy to the fasta files containing the genome that was used during the alignment step). These are needed by SNVMix. | |
8 | 11 |
9 Requirements | 12 Requirements |
10 ------------ | 13 ------------ |
11 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below | 14 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below |
12 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided | 15 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided |