Changes between Version 7 and Version 8 of SnpCallingPipeline


Ignore:
Timestamp:
Sep 22, 2010 5:22:39 PM (14 years ago)
Author:
Leon Mei
Comment:

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  • SnpCallingPipeline

    v7 v8  
    4646=== 3) Alignment] ===
    4747
    48 '''The three commands in this section are identical. Copy&Paste error?'''
     48'''The three commands in this section are identical. Copy&Paste error?  -- Leon'''
    4949
    5050To align the reads to a reference genome the GATK uses BWA. The indices used for this step were already made for an earlier Galaxy project. GATK uses an own version of BWA which doesn’t support multiple threading yet. To overcome this problem alignment was performed using the standard BWA. The following command was executed:'''''''