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, 14:37, 13 November 2014
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− | '''Note:''' the latest version of this practical is available at: [[SeqShop: Sequence Mapping and Assembly Practical]] | + | '''Note:''' the latest version of this practical is available at: [[SeqShop: Variant Calling and Filtering for SNPs Practical]] |
| * The ones here is the original one from the June workshop (updated to be run from elsewhere) | | * The ones here is the original one from the June workshop (updated to be run from elsewhere) |
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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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− | This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]] | + | This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014|Alignment Tutorial]] |
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| {{SeqShopRemoteEnv}} | | {{SeqShopRemoteEnv}} |
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| Per sample BAM files contain sequence reads that are mapped to positions in the genome. | | Per sample BAM files contain sequence reads that are mapped to positions in the genome. |
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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, June 2014#BAM_Files|SeqShop Aligment: BAM Files]] |
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− | 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. | + | For this tutorial, we will use the 4 BAMs produced in the [[SeqShop: Sequence Mapping and Assembly Practical, June 2014]] as well as with 58 BAMs that were pre-aligned to that 1MB region of chromosome 22. |
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| === Reference Files === | | === Reference Files === |
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| We will use the same configuration file as we used yesterday in GotCloud Align. | | We will use the same configuration file as we used yesterday in GotCloud Align. |
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− | See [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#GotCloud Configuration File|SeqShop: Alignment: GotCloud Configuration File]] for more details | + | See [[SeqShop:_Sequence Mapping and Assembly Practical, June 2014#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). | | * Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). |
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| </ul> | | </ul> |
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− | Let's take a look at that interesting location we found in the [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#Accessing_BAMs_by_Position|alignment tutorial]] : chromosome 22, positions 36907000-36907100 | + | Let's take a look at that interesting location we found in the [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014#Accessing_BAMs_by_Position|alignment tutorial]] : chromosome 22, positions 36907000-36907100 |
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| Use tabix to extract that from the VCFs: | | Use tabix to extract that from the VCFs: |