lizhichao
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Activity overview
Latest activity by lizhichao-
lizhichao created a post,
Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz is suitble for WGS VQSR?
AnsweredREQUIRED for all errors and issues: a) GATK version used:GATK4.2.2b) Exact command used: VariantRecalibrator --resourcec) Entire program log: I noticed that the ExAC runner the VQSR with Axiom_Exom...
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lizhichao commented,
Thanks for your answer!
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lizhichao commented,
if I compare two sample from two individual vcfs, then the above explanation is suited for that? Does the Site level calculate the REF/ATL difference of overlap sites of the two vcfs? the Genotype...
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lizhichao commented,
Sorry ，I cant get the difference between the genotype level and site level. By the way ,I did noticed that some paper calculate the precision at variant calls and genotype level .But I think the g...
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lizhichao created a post,
How to evlauate the result: GenotypeConcordance or Concordance
AnsweredREQUIRED for all errors and issues: a) GATK version used:gatk-4.1.7 b) Exact command used:/zfssz2/ST_MCHRI/BIGDATA/USER/liupanhong/Src/gatk-4.1.7.0/gatk --java-options -Xmx3G GenotypeConcordance \-...
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lizhichao commented,
Thanks， your repsponse is the exact answer to what i concerned. So I don't have to manually set the --ploidy when I run joint-calling with different samples input.
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lizhichao created a post,
pooled experiment means
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):b) What does ...
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lizhichao created a post,
GATK GenotypeGVCFs --sample-ploidy
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used:GATK 4.1.2b) Exact command used: GATK GenotypeGVCFs --sample-ploidy c) Entire error log: If not an error, choose a catego...
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lizhichao commented,
Thanks,I get what you means
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lizhichao commented,
I just want to study the homozygous deletion and heterozygous deletion of CNV genotyping in population,to find some assosication.