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GotCloud: GenomeSTRiP Pipeline

1,928 bytes added, 16:42, 10 February 2015
Input Data
== Input Data ==
== Input Data==
* [[#BAM Files|Aligned/Processed/Recalibrated BAM files]]
* [[#BAM List File|BAM list file containing Sample IDs & BAM file names]]
* [[#Reference Files|Reference files]]
* [[#Configuration File|Configuration file to override default options]]
=== BAM Files ===
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls. Generating these BAM files from original FASTQs is automatically done as part of the [[Alignment Pipeline]] of GotCloud.
=== BAM List File ===
* Automatically created when running the GotCloud [[Alignment Pipeline]]
* Each line of the BAM list file represents a single individual
# sample id
# comma separated population labels (optional column)
# BAM File 1 (preferable to have full paths to BAM files)
# BAM File 2 (if more than 1 BAM per sample)
: # BAM File N (if more than 1 BAM per sample)
* Notes:
** tab delimited
** multiple BAMs per individual may be provided, but should all be on the same line of the list file
** population label is optional - it will default to <code>ALL</code>
*** only used by Thunder (part of ldrefine pipeline)
*** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample.
=== Reference Files ===
See [[GotCloud: Genetic Reference and Resource Files]] for detailed information about the multiple required reference files for the variant calling pipeline, including:
* How to obtain default references
* Configuration keys & default values
* How to generate your own references
* How to point GotCloud to your reference files
Required Reference File Types:
* [[GotCloud: Genetic Reference and Resource Files#Reference fasta Files|Reference fasta Files]]
=== Configuration File ===
{{:GotCloud: Configuration}}
'''Replace the specified paths to the path to these files.'''
== Running GotCloud/GenomeSTRiP ==