Mingzhou Fu
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Recent activity by Mingzhou Fu Sort by recent activity-
CalculateGenotypePosteriors prior - should population prior be supplied to a trio vcf?
AnsweredHi there, I'm following the genotype refinement workflow (https://gatk.broadinstitute.org/hc/en-us/articles/360035531432-Genotype-Refinement-workflow-for-germline-short-variants) and doing Calculat...
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joint call samples with different ploidy on chrX & chrY (males vs females)
AnsweredHi there, I'm using GATK4.2 to run germline variant discovery (SNV+small indel) for ~800 WES samples. I went through autosomal chr well, but had a question regarding joint variant call for chrX & c...
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countsN meaning & example
AnsweredHi there, I'm using gatk variantannotator to add some extra annotation to my vcf file, and got somehow unclear about the 'CountNs'. I've checked the doc https://gatk.broadinstitute.org/hc/en-us/art...
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HRun not found in vcf header or INFO
Answereda) GATK version used: 4.1.2.0 Hi, I'm following GATK germline short variant discovery pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-...
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combineGVCF errors and questions: inconsistent references & combineGVCF twice
Hi there, Over the conversations in https://gatk.broadinstitute.org/hc/en-us/community/posts/4404389488923-GenotypeGVCFs-only-accepts-single-combinedGVCF-CombineGVCFs-genomicsdb-errors-interval-lis...
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GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset
AnsweredHi there, I have ~3000 samples (WES) and want to put them into GenotypeGVCFs for variant calling. I read the document and seemed GenotypeGVCFs only takes a single combined GVCF either by CombineGVC...
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What intervals to use in HaplotypeCaller & GenotypeGVCF for exome data sequenced with different capture kits
AnsweredHi there, I'm new to sequencing data analysis and hope someone can help with the --intervals option in HaplotypeCaller & GenotypeGVCF. I'm using GATK4.1.2.0 I sent my samples from the same cohort f...