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imputation and changing genotypes in Beagle and FImpute

beagle 4.0 fimpute imputation genotypes written 3.2 years ago by Wietje • 220 • updated 3.2 years ago by Shab86 • 270

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Beagle 4.0 Imputation - Warning: Skipping VCF record with no data

beagle 4.0 imputation vcf-file written 3.2 years ago by Wietje • 220 • updated 3.2 years ago by Pierre Lindenbaum ♦ 134k

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Recent Replies

C: How do I effectively automate BLAST searches without using a local database? by Malcolm.Cook • 1.2k
it is possible to limit the subset of nr searched in a way relevant to the OPs application by [Li...
C: How do I effectively automate BLAST searches without using a local database? by Malcolm.Cook • 1.2k
I am unfamiliar with using the python wrapper to blast+ command line. Regardless... I question...
C: KEGG enrichment pathway by rpolicastro ♦ 3.9k
There doesn't appear to be KEGG or Reactome entries for wheat, but there is GO ontology data avai...
C: How to filter vcf file on minimum genotype depth and quality for each sample by shinken123 • 100
FMT is for Format, you can find more info here: https://www.biostars.org/p/350919/
C: Gene expression heatmap following pseudotime analysis by rpolicastro ♦ 3.9k
Yep, the code is essentially calculating a smoothed average, and then sorting the genes based on ...
C: Gene expression heatmap following pseudotime analysis by Vitis • 2.4k
It's a brilliant solution! So it basically smooths the expression across features, then sorts the...
A: Error on Linear regression bulkRNAseq by rpolicastro ♦ 3.9k
prova$sex <- factor(prova$treatment, levels=c("F","M")) should be prova$sex <- ...
A: from phased SNPs to haplotype blocks (or phase sets) by Peter Chung • 130
maybe HAPCUT2 ? ./build/HAPCUT2 --fragments fragment_file --VCF variants.vcf --output haplotype_...
C: Annotating reads with the name of the feature to which they map by lech.kaczmarczyk • 0
Thanks a lot for clarification @A. Dominguez!
C: PCA plotting using DESEq2 pipeline by GenoMax ♦ 96k
This comment belongs under @ATpoint's comment in answer below. Please don't use `SUBMIT ANSWER` ...
A: PCA plotting using DESEq2 pipeline by aranyak111 • 0
Using this option I found the following results. PC1 PC2 group condition ...
C: How to interpret the gene level copy number file generated by ASCAT2 on GDC? by Kevin Blighe ♦ 71k
I have made an attempted answer, here: https://www.biostars.org/p/494728/#494755

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