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  • Protocol for finding variants in GATK

    Hi,

    I'm looking for a way to use GATK for finding variants. Unfortunately, their documentation is poor and misleading. The commands that they present on their presentation slides are out-of-dated.

    Can anyone post a simple working script or protocol for GATK given a raw BAM file?
    Last edited by student-t; 03-26-2015, 04:28 PM.

  • #2
    What documentations are you referring to?
    Although I agree that information is sometimes hard to find on their website, I personally think you'll have a hard time to find something with a better documented workflow than "GATK variant calling" in the world of bioinformatics.
    Have a look at this site which contains highly detailed presentation slides on how to use GATK from Sep 2014. https://www.broadinstitute.org/gatk/...ations?id=4768

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    • #3
      I have read the documentation but still having problems. What I'm doing now is that, I'm simulating variants, mutations etc from a reference genome. I'd expect I'd see something from the GATK tool. I ran through the pipeline but my resulting VCF file contains headers but no data. The problem is that I don't know whether I've screwed up my data or the way I'm using GATK is simply wrong. If there was a known protocol, then I could compare my steps with it.... Can anybody take a quick look at what I've done? It's paired-reads.

      Here's my pipeline:

      - silico.fa is my reference genome



      - Create Index for FASTQ

      samtools faidx silico.fa

      - Generate a sequence dictionary

      java -jar ../../Tools/Picard/picard.jar CreateSequenceDictionary REFERENCE=silico.fa OUTPUT=silico.dict

      - Alignment

      bwa mem -t 20 -M -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1' silico_index reads/simulated_1.fastq reads/simulated_2.fastq > aligned.sam

      - Sort SAM to BAM

      java -jar ../../Tools/Picard/picard.jar SortSam INPUT=aligned.sam OUTPUT=sorted.bam SORT_ORDER=coordinate

      - Mark Duplicates

      java -jar ../../Tools/Picard/picard.jar MarkDuplicates INPUT=sorted.bam OUTPUT=marked.bam METRICS_FILE=metrics.txt

      - Build BAM Index

      java -jar ../../Tools/Picard/picard.jar BuildBamIndex INPUT=marked.bam

      - RealignerTargetCreator

      java -jar ../../Tools/GATK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R silico.fa -I marked.bam -o realigner.intervals

      - IndelRealigner

      java -jar ../../Tools/GATK/GenomeAnalysisTK.jar -T IndelRealigner -R silico.fa -I marked.bam -targetIntervals realigner.intervals -o realigned.bam

      - Haplotype Analysis

      java -jar ../../Tools/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R silico.fa -I realigned.bam --genotyping_mode DISCOVERY --heterozygosity 0.01 --defaultBaseQualities 30 -o haplotype.vcf
      Last edited by student-t; 03-27-2015, 11:49 PM.

      Comment


      • #4
        The question becomes how the simulated reads were made.

        Comment

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