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  • GATK Based Variant calling STEPS

    Hello,

    I am working on putting together a workflow for calling variants using Haplotype called in GATK:

    The process follow I currently follow is as below:

    Mapping : BWA- MEM

    Picard :SORT SAM: java -jar /opt/NGSTools/picard-tools-1.118/SortSam.jar INPUT=clean.bam OUTPUT=samsorted.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENTAdd/Replace GroupsReOrderSAM

    ++++++++++++++++++

    GATK

    1) RealignerTargetCreator
    2) IndelRealigner
    3) HaplotypeCaller :
    java -jar /opt/NGSTools/GATK-3.2.2/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/data/GATK_test/gatk/ucsc.hg19.fasta -I realigned.bam -stand_call_conf 30 -stand_emit_conf 10 --min_base_quality_score 15 -o haplotype.raw.snps.indels.vcf

    +++++++++++++++++++++++++++++++++++++++++++++++

    Can any one help me to check if the above process flow looks good to determine variants (gene panel and exome based experiments)?

    Suggestion would be highly appreciated!
    Thanks,
    Satish

  • #2
    Dear Satish

    I think if you follow the guidelines given here (as you are focusing on GATK):

    then you cannot go wrong.
    Good luck.

    Comment

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