Field -Ye Tian
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Activity overview
Latest activity by Field -Ye Tian-
Field -Ye Tian commented,
Dear GATK developers, I have processed a pair of Tumor/normal tissues that are WES'ed. I have followed the whole process of analysis and acquired the annotated .maf result. After going through it,...
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Field -Ye Tian commented,
Hi Genevieve, Thank you for the reply. I'd like to quickly update that the resources you provided are useful. Just a quick note for whomever encountered the same issue, the GATK germline resource...
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Field -Ye Tian commented,
Hi Genevieve, Thank you for the prompt reply. It seems from your reply that GRCh38 and HG38 are slightly different. I've been searching webpages but all referred the two identically. I'd like to c...
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Field -Ye Tian created a post,
Mutect2 panel of normals and germline source files with incompatible contigs
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1b) Exact command used: gatk Mutect2 -R ~/shared/Genome_Refs/GCF_000001405.39_GRCh38.p13_genomic.fna -I ~/shared/l...
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Field -Ye Tian commented,
As a quick update, align with the latest grch38patch13 didn't solve the above-mentioned problem.
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Field -Ye Tian commented,
Dear GATK group, I have encounter a similar (if not the same) problem running the Mutect2 program. It says "A USER ERROR has occurred: Input files reference and features have incompatible contigs:...
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Field -Ye Tian commented,
Hi Genevieve, The problem I posted can be solved by changing the downloaded file's suffix to .vcf.gz and then unzip it. Although I have encountered another issue, namely Input files reference and ...
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Field -Ye Tian commented,
Hi Genevieve, For some weird reason, I saw the file listed under the name "1000g_pon.hg38.vcf.gz" but when I downloaded it, I automatically got the file "somatic-hg38_1000g_pon.hg38.vcf". Similar ...
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Field -Ye Tian commented,
Hi Genevieve, I met a rather similar problem running MuTect2. I found from other threads that both files of 1000g_pon.hg38.vcf.gz and af-only-gnomad.hg38.vcf.gz are not strictly required but wil...
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Field -Ye Tian commented,
I have later on figured out that the dictionary can also be generated with the Picard-tools with the command java -jar picard.jar CreateSequenceDictionary \ R=reference.fasta \ O=refere...