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| 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 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-aligned. | + | 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-aligned to that 1MB region of chromosome 22. |
| | | |
| === Reference Files === | | === Reference Files === |
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| #* hapmap - used as likely true positives for SVM filtering and for generating summary statistics | | #* hapmap - used as likely true positives for SVM filtering and for generating summary statistics |
| #* dbsnp - used 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: | | 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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| </div> | | </div> |
| </ul> | | </ul> |
− |
| |
− | === 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 === | | === GotCloud BAM Index File === |
| The BAM index file points GotCloud to the BAM files | | The BAM index file points GotCloud to the BAM files |
− | * Alignment pipeline generates for you | + | * generated by the alignment pipeline |
− | * Tab delimited
| |
| | | |
| Look at the BAM index file the alignment pipeline generated | | Look at the BAM index file the alignment pipeline generated |
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| </ul> | | </ul> |
| </ul> | | </ul> |
| + | |
| + | === 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 == | | == Run GotCloud SnpCall == |