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Revision as of 14:34, 13 November 2014
, 14:34, 13 November 2014no edit summary
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 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.
=== Reference Files ===
=== Reference Files ===
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.
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).
