User: Vivek
Vivek • 2.4k
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PhD candidate, Genetics of complex traits.
Posts by Vivek
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... Hi,
I'm trying to implement a polygenic score pipeline in WDL and I'm quite new to this pipeline management.
The first step of the pipeline takes a file of GWAS summary statistics and splits it by chromosome.
The corresponding wdl task:
task split {
input {
File gwas
...
written 4 weeks ago by
Vivek • 2.4k
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answer
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... You need to either compute a kinship coefficient or tally the number of mendelian violations. Check KING for doing the analysis. You might need to convert your VCF to PLINK format. ...
written 3 months ago by
Vivek • 2.4k
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... I tried to subset the reference but beagle's default mode is to impute in 40 mb chunks with a 4 mb overlap so if I were to try and replicate that for my 10k masked SNPs, it becomes cumbersome enough to do whole genome imputation. ...
written 3 months ago by
Vivek • 2.4k
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... Hi,
I wish to compare the performance of two genotyping chips for phasing and imputation protocols on a dataset. To do this, I have masked a small set of 10k SNPs in the dataset from each chip prior to pre-phasing and phased each dataset using three different tools. Now due to resource constraints ...
written 3 months ago by
Vivek • 2.4k
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Comment:
C: Position error using write.plink
... Can you also post the map file you are using here? `snp.data = smc_test$map`
Is there a discordance between your snp.data and this map? ...
written 18 months ago by
Vivek • 2.4k
1
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957
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... I'm not sure what you mean by p_hat, the admixture QC is done with some PCA analysis and a reference population like 1000 genomes. There must be a tutorial on biostars if you search for it. You remove any samples related more than third degree using KING for kinship analysis. ...
written 18 months ago by
Vivek • 2.4k
1
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957
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... When you use a linear model to check for association (Y = XB + E) the core assumption is that the elements of Y are independent, that's why you check for kinship and admixture and remove any that violate those assumptions. ...
written 18 months ago by
Vivek • 2.4k
3
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1
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957
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... The phase and impute strategy would work if you have a genome wide array of markers. There won't be enough genome wide SNP coverage to impute accurately if all you have is an exome array. The other option is to go with weighted burden tests, finding something from them is a question of how much powe ...
written 18 months ago by
Vivek • 2.4k
0
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585
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... If this is intended towards research, history of parental diagnosis would appear to be useful. ...
written 19 months ago by
Vivek • 2.4k
1
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590
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Comment:
C: vcf file processing
... There are more elegant solutions if you can do some scripting but here's a crude workflow:
If you have one line per gene in the bed file, you can initially split the BED file into one file per gene like this:
split -l 1 Genes.bed Genes-
Depending on the number of genes, you might produce a l ...
written 24 months ago by
Vivek • 2.4k
Latest awards to Vivek
Scholar
3 months ago,
created an answer that has been accepted.
For A: Different annotation gtf file in Tophat2 and Cufflink
Scholar
6 months ago,
created an answer that has been accepted.
For A: Identify overlapping coordinates
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
Good Answer
20 months ago,
created an answer that was upvoted at least 5 times.
For A: retrieving from ExAC in VCF format
Commentator
2.2 years ago,
created a comment with at least 3 up-votes.
For C: data science courses, offered by John Hopkins University at Coursera
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
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2.6 years ago,
asked a question that was upvoted at least 5 times.
For Identifying De Novo Variants In Trio Data
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For C: data science courses, offered by John Hopkins University at Coursera
Popular Question
2.6 years ago,
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For Bioinformatics Programmer at Baylor College of Medicine, Houston TX
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2.6 years ago,
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For Identifying De Novo Variants In Trio Data
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2.7 years ago,
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For A: VCF files: Change Chromosome Notation
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
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2.8 years ago,
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For A: VCF files: Change Chromosome Notation
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2.8 years ago,
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For A: Phasing trios for identification of denovo variants
Teacher
2.8 years ago,
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For A: Identify overlapping coordinates
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2.8 years ago,
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For A: Identify overlapping coordinates
Teacher
3.0 years ago,
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For A: Identify overlapping coordinates
Teacher
3.0 years ago,
created an answer with at least 3 up-votes.
For A: Identify overlapping coordinates
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3.2 years ago,
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For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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3.3 years ago,
created a post with more than 5 votes.
For A: Phasing trios for identification of denovo variants
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