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ShapeIT output File Allele Info

shapeit vcf shapeit3 impute2 shapeit2 written 8 weeks ago by prmshakya • 0

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198

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Shapeit2 cannot open reference panel

gwas phasing shapeit2 written 11 months ago by sunnysean • 20 • updated 11 months ago by Kevin Blighe ♦ 69k

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471

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Shapeit2 - malformed hap file output?

phasing snp shapeit2 written 2.3 years ago by mstagliamonte • 0

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693

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Phasing Confidence Values using Shapeit2

haplotype estimation wgs phasing shapeit2 written 2.6 years ago by Mike Vermeulen • 10

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2.0k

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5 follow

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Convert numeric alleles into letters

gwas rehh shapeit2 written 3.9 years ago by Gennady Khvorykh • 90

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2.1k

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shapeit2 pre-phasing error- empty hap file

pre-phasing gwas shapeit2 written 4.5 years ago by Mamta • 460 • updated 4.4 years ago by Biostar ♦♦ 20

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Recent Replies

A: DiffBind dba.analyze never finishes by Rory Stark • 900
What platform are you running (Windows, Mac, Linux)? It would help to see the output of `sessionI...
C: The Biostar Handbook. A bioinformatics e-book for beginners. by Michael Dondrup ♦ 48k
Hello and Happy New Year! After having used the CVGA book with very good results last year I wou...
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Thank you for your input. I also encountered some posts stating that. But if its memory problem, ...
C: About shiny HTML issues by 153348734 • 0
Thank you, I have a post in stackoverflow, https://stackoverflow.com/questions/65770117/how-do-i-...
C: About shiny HTML issues by e.rempel • 980
Sorry, but this is just not enough information. Furthermore, I think, it is more helpful to post ...
C: Non-coding region of WGS by FL512 • 0
Thank you very much. That was also I was thinking of but I did not know how to do it because of t...
C: Non-coding region of WGS by ATpoint ♦ 44k
Extract the non-UTR exons in BED format, use `bedtools complement` to get the complement of the e...
C: Error in extracting SRA file: symbol lookup error by marongiu.luigi • 520
Does not matter. I reinstalled all SRAtoolkit and now it works... case closed.
C: Running GSVA using open source RNA seq data by Lluís R. • 970
Could you post the errors or messages you get ? "Having issues making/getting" doesn't help much ...
A: Qualimap: java.lang.RuntimeException: The raw data doesn't exist for sample ? by dare_devil • 770
Summary: To run `multi-bamqc` in `qualimap`, you should have a `bed` file containg six columns: ...
C: ColSideColors' must be a character vector of length ncol(x) by Kevin Blighe ♦ 69k
Can you try to re-format your post? - thanks!
C: GSEA from broad institute normalization method by Kevin Blighe ♦ 69k
Yep, but you can also use the normalised counts, accessible via: counts(dds, normalized = TR...

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