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  • GATK command options

    I just want to be sure that I am interpreting the below correct:

    In this GATK command the -L 20 gives the chromosome 20 only and if all chromosomes were used then the -L can be removed.

    The -known is only used if your organism has a file (maybe hg19 does, but I have to search). Is it a text file?

    Code:
    java -jar GenomeAnalysisTK.jar \ 
        -T RealignerTargetCreator \ 
        -R reference.fa \ 
        -I dedup_reads.bam \ 
        [B][B]-L 20 \ [/B][/B]       (chromomosome 20 only)
        [I]-known gold_indels.vcf \ [/I]   (optional) 
        -o realignment_targets.list
    
    Expected Result
    
    This creates a file called realignment_targets.list containing the list of intervals that the program identified as needing realignment within our target, chromosome 20.
    
    The list of known indel sites (gold_indels.vcf) are used as targets for realignment. Only use it if there is such a list for your organism.
    In the below GATK command:

    Code:
    java -jar GenomeAnalysisTK.jar \ 
        -T BaseRecalibrator \ 
        -R reference.fa \ 
        -I realigned_reads.bam \ 
        -L 20 \ 
        -knownSites dbsnp.vcf \ 
        -knownSites gold_indels.vcf \ 
        -o recal_data.table
    t he -L20 and -known do the same as in the previous command. Thank you .

  • #2
    "gold_indels.vcf" is a VCF; see here for the latest specification.

    Comment


    • #3
      Concerning your question: No, "L" restricts the variant calling to a certain region (in your example chr20); "known" specifies a file containing known variants - these files contain variant info over the whole genome.

      The Broad institute offers a resource bundle for hg19 which also include the known variants (https://www.broadinstitute.org/gatk/download/)

      Comment


      • #4
        Thank you .

        Comment

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