Changes between Version 4 and Version 5 of SOPs/callingSNPs


Ignore:
Timestamp:
07/09/13 13:30:58 (12 years ago)
Author:
thiruvil
Comment:

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  • SOPs/callingSNPs

    v4 v5  
    2323
    2424
     25=== GATK Overview ===
     26
     27  * Map reads to reference after QC'ing
     28  * Mark duplicates: sequencing errors can propagate due to amplification (use Picard Tools)
     29  * Indel-based realignment: misalignment by aligner is likely to occur near indels (use RealignerTargetCreator and IndelRealigner)
     30  * Base quality recalibration: base quality score will be made more accurate (use BaseRecalibrator and PrintReads)
     31  * Run UnifiedGenotyper to call variants
    2532
    2633== Filtering SNPs ==