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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Problem with Haplotypecaller

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5 comments

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    Bhanu Gandham

    Hi,

     

    Please check the forum. This issue has been solved a few times already.

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    Khagani Eynullazada

    Dear Bhani

     

    Thanks for the comment. I searched for all post in this forum but I could not find the relevant one. I have seen similar posts in other forums and GATK team member's solutions to their problem, like using the same reference to align the genome or reordering the bam file according to the reference genome. However, none of them helped in my situation. I would highly appreciate if you point me to the post you think is relevant to my issue.

     

    I am looking forward to hearing from you.

     

    Best

     

    Khagani

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    Khagani Eynullazada

    Thanks for the link. As I mentioned above I have already tried doing realignment and it did not solve my issue. 

     

    I appreciate your help 

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    Bhanu Gandham

    Hi Khagani Eynullazada

     

    You are providing a .bai file as input instead of a .bam file.

    See your command posted above:

    "Command I execute:./gatk-4.1.7.0/gatk HaplotypeCaller -R mm10.fasta -I A2S_Day6.srt.bam.bai -O variants.vcf"

     

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