Mingzhou Fu
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Activity overview
Latest activity by Mingzhou Fu-
Mingzhou Fu created a post,
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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Mingzhou Fu commented,
Okay.... I did some research and found combinegVCF & genotypeGVCF can deal with samples with mixed ploidy (https://gatk.broadinstitute.org/hc/en-us/articles/360035889691-Does-GATK-work-on-non-diplo...
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Mingzhou Fu created a post,
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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Mingzhou Fu commented,
Got it! Thank you for the links! Now I understand this annotation.
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Mingzhou Fu created a post,
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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Mingzhou Fu commented,
Thank you!
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Mingzhou Fu commented,
Hi there, I actually found the Hrun (named HomopolymerRun) in GATK3.8. I tried to run GATK3.8 VariantAnnotator on my VCF file generated by GATK4. Here's the command module load gatk/3.8.0 ref_ge...
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Mingzhou Fu created a post,
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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Mingzhou Fu commented,
I see. Thank you very much for the explanation :)
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Mingzhou Fu commented,
Gotcha! Thank you Genevieve! Last question regarding your previous suggestions - " I think for your case I would recommend running CombineGVCFs for all samples, but separating the runs by chromoso...