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Examining GotCloud SnpCall Input files
For a reminder on how to look at/read BAM files, see: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#BAM_Files|SeqShop Aligment: BAM Files]]
For this tutorial, we will use the 4 BAMs produced in the [[SeqShop: Sequence Mapping and Assembly Practical]] as well as with 58 BAMs that were pre-alignedto that 1MB region of chromosome 22.
=== Reference Files ===
#* hapmap - used as likely true positives for SVM filtering and for generating summary statistics
#* dbsnp - used for generating summary statistics
 
We looked at them yesterday, but you can take another look at the chromosome 22 reference files included for this tutorial:
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=== GotCloud Configuration File ===
We will use the same configuration file as we used yesterday in GotCloud Align.
 
See [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#GotCloud_Configuration_File|SeqShop: Alignment: GotCloud Configuration File]] for more details
* Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X).
 
For more information on configuration, see: [[GotCloud:_Variant_Calling_Pipeline#Configuration_File|GotCloud snpcall: Configuration File]]
* Contains information on how to configure for exome/targeted sequencing
=== GotCloud BAM Index File ===
The BAM index file points GotCloud to the BAM files
* Alignment generated by the alignment pipeline generates for you* Tab delimited
Look at the BAM index file the alignment pipeline generated
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=== GotCloud Configuration File ===
We will use the same configuration file as we used yesterday in GotCloud Align.
 
See [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#GotCloud Configuration File|SeqShop: Alignment: GotCloud Configuration File]] for more details
* Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X).
 
For more information on configuration, see: [[GotCloud:_Variant_Calling_Pipeline#Configuration_File|GotCloud snpcall: Configuration File]]
* Contains information on how to configure for exome/targeted sequencing
== Run GotCloud SnpCall ==

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