User: nkausthu

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nkausthu20
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Posts by nkausthu

<prev • 47 results • page 4 of 5 • next >
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Comment: C: Annotation of XHMM VCF file (CNV analysis)
... Right now I am also checking manually by downloading the complete set of cnv from DGV. But wanted to figure out whether it could be automated. Looking at OMIM genes is one thing I thought of doing to identify cnvs for know disease causing genes. Again cnv of a new gene which is not yet associated ...
written 2.5 years ago by nkausthu20
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Comment: C: Annotation of XHMM VCF file (CNV analysis)
... Basically I would like to know which all are the gene or genes involved in deletions or duplications. Along with that I need to know its a rare or a common cnv.. ...
written 2.5 years ago by nkausthu20
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Annotation of XHMM VCF file (CNV analysis)
... Hi, I have XHMM generated VCF file which contains the CNVs from exomes of 200 individuals. It would be really great if someone can suggest me how to annotate this VCF (I have annotated using annovar but I don't know whether this is best way to do CNV annotation). Is there any methodology availabl ...
exome annotation vcf xhmm cnv written 2.5 years ago by nkausthu20
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Comment: C: Allele frequency calculation
... just consider the following 3 scenarios 1. 3 related individuals - het/het/het - this will be taken as 1 allele count 2. 3 related individuals - hom/hom/hom - this will be taken as 2 allele counts 3. 3 related individuals - het/hom/het - what will be the allele count in this scenario ...
written 3.3 years ago by nkausthu20
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Comment: C: Allele frequency calculation
... You are absolutely right!! Removing redundant variants from related individual is something I though about but again the problem is which zygosity I should keep. eg : same variant in het/het/hom in three related individuals and which variant I will keep and which will I remove? . As you already to ...
written 3.3 years ago by nkausthu20
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Comment: C: Allele frequency calculation
... I would like to make an in-house variant database from our available exomes and the corresponding allele frequencies will be used to filter the variants. It would be helpful if you can give some further information about the methods to adjust relatedness. Thank you .. ...
written 3.3 years ago by nkausthu20
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Comment: C: Allele frequency calculation
... Actually I would like to know if I include all these related individuals along with unrelated individuals for calculating the allele frequency will it be biased? Or is there any statistical way to avoid this bias? ...
written 3.3 years ago by nkausthu20
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Allele frequency calculation
... I have ~200 exomes which includes related and unrelated individuals. I have done the joint genotype calling and calculated the allele frequency using VCFtools. But as its a mixed population what is the ideal way to calculate allele frequency?. I would like to make an in-house variant database from ...
allele frequency joint genotype calling written 3.3 years ago by nkausthu20
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Comment: C: Number of homozygous and heterozygous variants
... Ok..Probably I can discard these genotypes while taking the count. ...
written 3.3 years ago by nkausthu20
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Comment: C: Number of homozygous and heterozygous variants
... Thanks for the reply .. Then why can't we consider the variant CT -> 1/2 as heterozygous? These scenarios are biologically relevant ? ...
written 3.3 years ago by nkausthu20

Latest awards to nkausthu

Popular Question 12 months ago, created a question with more than 1,000 views. For Tools for visualization of CNVs called by XHMM
Popular Question 16 months ago, created a question with more than 1,000 views. For Annotation of XHMM VCF file (CNV analysis)
Popular Question 16 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 19 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 19 months ago, created a question with more than 1,000 views. For Number of homozygous and heterozygous variants

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