Xin Zheng
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Activity overview
Latest activity by Xin Zheng-
Xin Zheng commented,
Hi David-Benjamin I have read https://github.com/broadinstitute/gatk/pull/6821 and in use gatk-4.1.9.0, but there are still some sites that cannot be detected (KRAS-vaf 0.01). So I tested some ...
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Xin Zheng commented,
Hi David Benjamin, I have encountered the same issue that Saba describes in this thread with a couple of low VAF (2%) variants, and the raw data Quality value was good. Waiting for the result. Thanks.
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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
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,
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,
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
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/...