User: alerodriguez

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alerodriguez70
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Posts by alerodriguez

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Answer: A: filter out related individuals from a vcf file using Plink or Hail
... Kevin thank you very much, however; what I want to do is to: 1.Remove related individuals 2.Remove individuals with a specific phenotype for which I have a txt file. If I understand correctly your code changes vcf to plink files only right? How can I filter out individuals as in 1,2.? Also, I don't ...
written 4 weeks ago by alerodriguez70
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filter out related individuals from a vcf file using Plink or Hail
... I have a data set for 11,000 individuals and would like to filter out related individuals and also based on a phenotype. I have a vcf file format and prefer to work with Plink, Hail or vcftools? ...
vcf file hail related individuals plink written 4 weeks ago by alerodriguez70
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Comment: C: FastQTL - GNU Scientific Library (GSL) Domain Error
... Going trough Ongen et al. 2016 I agree with you that control is at the gene level not based on the amount of SNPs. However, I still struggle to understand why since this step is still considered "multiple testing". Thank you so much for your help! ...
written 6 weeks ago by alerodriguez70
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Comment: C: FastQTL - GNU Scientific Library (GSL) Domain Error
... Thank you very much for your answer mobius, I have a follow-up question. If I'm only testing a restricted number of SNPs going into the analysis e.g 240 will program computed the BETA p-value based on the number of SNPs in my vcf file (0.05/240= 0.0002083333 )? Or in some way compute a genome-wide B ...
written 6 weeks ago by alerodriguez70
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Answer: A: FastQTL - GNU Scientific Library (GSL) Domain Error
... Thank you very much for your answer mobius, I have a follow-up question. If I'm only testing a restricted number of SNPs going into the analysis e.g 240 will program computed the BETA p-value based on the number of SNPs in my vcf file (0.05/240= 0.0002083333 )? Or in some way compute a genome-wide B ...
written 6 weeks ago by alerodriguez70
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Comment: A: Vcflib Documentation
... I need to filter my vcf file to include only variants that have at least 30 individuals in each of the possible genotypes is it possible to do this with Vcflib. Thanks! ...
written 7 weeks ago by alerodriguez70
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Comment: C: vcf file filter
... I am getting the following error: NameError Traceback (most recent call last) in () 1 ----> 2 vds = hc.import_vcf('x.clean.tidy.vcf') NameError: name 'hc' is not defined In [22]: ...
written 7 weeks ago by alerodriguez70
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Comment: C: FastQTL - GNU Scientific Library (GSL) Domain Error
... Thank you very much for your insight, very helpful. Can you please also demystify whether it is necessary to consider the bata approximated p-value: For example, a SNP that is significant by the PermP but not by BETA would remain significant? P PermP FWER BETA ...
written 7 weeks ago by alerodriguez70
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vcf file filter
... I need to filter my vcf file to include variants with at least 30 individuals in each of the possible groups: major allele homozygous, heterozygous, and minor allele homozygous; would be grateful for any input. Thanks! ...
vcf filter snps minor allele homozygotes written 7 weeks ago by alerodriguez70 • updated 7 weeks ago by Pierre Lindenbaum102k
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Comment: A: Filtering Vcf File
... I need to filter my vcf file to include variants with at least 30 individuals in each of the possible groups: major allele homozygote, heterozygote, and minor allele homozygotes; would be grateful for any input. Thanks! ...
written 7 weeks ago by alerodriguez70

Latest awards to alerodriguez

Supporter 11 weeks ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For merging two bigwig files

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