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Krithika_Subramanian

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Latest activity by Krithika_Subramanian
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    Krithika_Subramanian commented,

    Hi Pamela Bretscher, Thank you for moving this post to the general discussion.  After running "PostprocessGermlineCNVCalls" module which is the last step of this Germline CNV caller, it generates o...

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    Krithika_Subramanian commented,

    Attached screenshot  

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    Krithika_Subramanian created a post,

    GATK Germline CNV calling

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: GATK-4.1.8.0b) Exact command used: Followed this post workflow (https://gatk.broadinstitute.org/hc/en-us/articles/360035...

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    Krithika_Subramanian commented,

    Hi Pamela, Thank you for your clarification. I have given specific parameters in my command for excluding, for example, QD <2.0, SOR > 3.0, MQ < 40.0 etc.  In my input, there are variants that have...

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    Krithika_Subramanian commented,

    Hi Pamela Bretscher, Thanks for your reply. Could you please explain me, how I can check whether VariantFiltration is applied for my data? Because there are 742,973 variants present before applying...

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    Krithika_Subramanian commented,

    Hi Pamela Bretscher, Thanks for your reply. Here I am providing a variant line, which has the value of ReadPosRankSum or MQRankSum. Also, I am not seeing any differences after applying this filtrat...

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    Krithika_Subramanian created a post,

    GATK Variant Filtration undefined variable

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.0b) Exact command used: gatk VariantFiltration -V Input_SNP.vcf -filter "QD < 2.0" --filter-name "QD2" -filter "QU...

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    Krithika_Subramanian created a post,

    GenomicsDB incremental error

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.4.1b) Exact command used: gatk GenomicsDBImport -V S1_Haplotypecaller.g.vcf -V S2_Haplotypecaller.g.vcf -V S3_Haplot...

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    Krithika_Subramanian created a post,

    GATK-CollectVariantCallingMetrics - regarding more information

    Can you please provide a) GATK version used : 4.1.2.0b) Exact GATK commands used : gatk CollectVariantCallingMetrics \       INPUT=${input_vcf} \       OUTPUT=${metrics_basename} \       DBSNP=${d...