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Manoj Kumar

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Latest activity by Manoj Kumar
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    Manoj Kumar created a post,

    Not getting vcf file

    1. Community
    2. Germline

    I am trying following commands to generate vcf file from HISAT2 generated alignment .sam file. I tried a lot but I am not able to figure out the issue. please advice. Command: ./gatk --java-options...

    • Manoj Kumar
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    Manoj Kumar commented,

    1. Community
    2. Other
    3. ERROR while calling variants...

    Hi I have fastq (MnION) file and a reference fasta file..I have still issue to not getting results ......  --FILE 1 @ID_5331388CTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTCTCCTCCACTCTGGGATGGGAATTC...

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    • Manoj Kumar
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    Manoj Kumar created a post,

    ERROR while calling variants...

    1. Community
    2. Other

    I am using gatk-4.1.7.0 version with following command, however I am getting error. please advice.... Command: gatk-4.1.7.0$./gatk HaplotypeCaller -R /home/kumarm/allan-work/RNASEq-alignment/ref_se...

    • Manoj Kumar
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