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Xin Zheng

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Latest activity by Xin Zheng
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    Xin Zheng created a post,

    When calling with polyN region of right mapping lead to loss of true pathogenic snp site

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    2. Somatic

    Can you please provide a) GATK 4.1.6.0b) command：gatk Mutect2 --f1r2-tar-gz HE0523-GW20T040B05_L2.mutect2.f1r2.tar.gz --panel-of-normals pon.vcf.gz --germline-resource af-only-gnomad.new.sites.hg19...

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    Xin Zheng commented,

    1. Community
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    3. GATK4.1.5 mutect2 output issue

    Bhanu Gandham Thank you for your advice. 1. When I use independent-mates, this unormal site be gone and the other sites look normal. Unfortunately I couldn't find parameters(2, 3)  in gatk4.1.5. Do...

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    Xin Zheng commented,

    1. Community
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    3. GATK4.1.5 mutect2 output issue

    Hi Bhanu Gandham Thanks for your help.Here is the bamout result, and I wonder why DP and other information is zero.

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    Xin Zheng created a post,

    GATK4.1.5 mutect2 output issue

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    2. Somatic

    When I use GATK4.1.5 wiht command line: /bioinfo/software/packages/gatk4/gatk-4.1.5.0/gatk Mutect2 -R /bioinfo/data/Genomes/NCBI/build37/Sequence/WholeGenomeFasta/human_g1k_v37.fasta -I bamclipper/...

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