From 5bc9ee67e20ed1a3070fe75764ba3f2801e5176d Mon Sep 17 00:00:00 2001 From: Retype GitHub Action Date: Wed, 4 Dec 2024 15:34:07 +0000 Subject: [PATCH] Refreshes Retype-generated documentation. Process triggered by pdimens. --- 404.html | 38 +- blog/feed.xml | 30 +- .../index.html | 58 +- blog/index.html | 85 +-- blog/simulate_diploid/index.html | 640 ---------------- .../index.html | 63 +- blog/sort_by_barcode/index.html | 485 ------------ blog/sv_pooling/index.html | 561 -------------- categories/guides/index.html | 85 +-- categories/index.html | 40 +- commonoptions/index.html | 168 ++--- development/index.html | 106 ++- haplotagdata/index.html | 66 +- index.html | 104 +-- install/index.html | 72 +- {troubleshooting => issues}/index.html | 195 ++--- {workflows => modules}/align/bwa/index.html | 101 +-- {workflows => modules}/align/ema/index.html | 118 +-- {workflows => modules}/align/index.html | 48 +- .../align/strobe/index.html | 104 +-- {workflows => modules}/deconvolve/index.html | 117 ++- {workflows => modules}/demultiplex/index.html | 90 +-- {workflows => modules}/impute/index.html | 348 ++++----- {workflows => modules}/other/index.html | 232 ++---- {workflows => 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57540 -> 0 bytes utilities/index.html | 589 --------------- workflows/assembly/index.html | 714 ------------------ workflows/metassembly/index.html | 644 ---------------- 70 files changed, 1500 insertions(+), 6938 deletions(-) rename blog/{filtering_snps => filteringsnps}/index.html (89%) delete mode 100644 blog/simulate_diploid/index.html rename blog/{software_environments => softwareenvironments}/index.html (88%) delete mode 100644 blog/sort_by_barcode/index.html delete mode 100644 blog/sv_pooling/index.html rename {troubleshooting => issues}/index.html (74%) rename {workflows => modules}/align/bwa/index.html (89%) rename {workflows => modules}/align/ema/index.html (88%) rename {workflows => modules}/align/index.html (90%) rename {workflows => modules}/align/strobe/index.html (90%) rename {workflows => modules}/deconvolve/index.html (87%) rename {workflows => modules}/demultiplex/index.html (88%) rename {workflows => modules}/impute/index.html (84%) rename {workflows => modules}/other/index.html (82%) rename {workflows => modules}/phase/index.html (88%) rename {workflows => modules}/preflight/index.html (90%) rename {workflows => modules}/qc/index.html (89%) rename {workflows => modules}/simulate/index.html (89%) rename {workflows => modules}/simulate/simulate-linkedreads/index.html (84%) rename {workflows => modules}/simulate/simulate-variants/index.html (83%) rename {workflows => modules}/snp/index.html (88%) rename {workflows => modules}/sv/index.html (90%) rename {workflows => modules}/sv/leviathan/index.html (90%) rename {workflows => modules}/sv/naibr/index.html (89%) delete mode 100644 static/assembly_multiqc.png delete mode 100644 static/assembly_quast.png delete mode 100644 static/depth_coverage.png delete mode 100644 static/depth_coverage.svg delete mode 100644 static/error_text.png delete mode 100644 static/favicon.svg create mode 100644 static/favicon_dark.png create mode 100644 static/logo_mini.png delete mode 100644 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  • diff --git a/blog/feed.xml b/blog/feed.xml index cdfc09916..9bc7d44f2 100644 --- a/blog/feed.xml +++ b/blog/feed.xml @@ -5,7 +5,7 @@ https://pdimens.github.io/harpy/blog/ Blog © Copyright 2024. All rights reserved. - Tue, 05 Nov 2024 00:00:00 GMT + Fri, 21 Jun 2024 00:00:00 GMT https://retype.com @@ -13,33 +13,9 @@ https://pdimens.github.io/harpy/blog/ https://pdimens.github.io/harpy/favicon.png - - Sort data by barcode - https://pdimens.github.io/harpy/blog/sort_by_barcode/ - Sorting data by linked-read barcode - Pavel Dimens - Tue, 05 Nov 2024 00:00:00 GMT - guides - - - Simulating variants - https://pdimens.github.io/harpy/blog/simulate_diploid/ - A realistic workflow to simulate variants - Pavel Dimens - Mon, 30 Sep 2024 00:00:00 GMT - guides - - - Pooling samples for SV calling - https://pdimens.github.io/harpy/blog/sv_pooling/ - Why pool samples for SV calling and when to do it - Pavel Dimens - Thu, 01 Aug 2024 00:00:00 GMT - guides - Choosing a software runtime method - https://pdimens.github.io/harpy/blog/software_environments/ + https://pdimens.github.io/harpy/blog/softwareenvironments/ Deciding between using Conda or Containers Pavel Dimens Fri, 21 Jun 2024 00:00:00 GMT @@ -47,7 +23,7 @@ Filtering Variants - https://pdimens.github.io/harpy/blog/filtering_snps/ + https://pdimens.github.io/harpy/blog/filteringsnps/ A gentle introduction to the wild world of filtering SNPs Pavel Dimens Wed, 05 Jun 2024 00:00:00 GMT diff --git a/blog/filtering_snps/index.html b/blog/filteringsnps/index.html similarity index 89% rename from blog/filtering_snps/index.html rename to blog/filteringsnps/index.html index 27d5421c7..5f9246be6 100644 --- a/blog/filtering_snps/index.html +++ b/blog/filteringsnps/index.html @@ -4,7 +4,7 @@ - + @@ -15,21 +15,21 @@ - + - + - + - + - + @@ -37,12 +37,12 @@ - + - + - - + +
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    Missing data is, frankly, not terribly useful. The amount of missing data you're willing to tolerate will depend on your study, but it's common to remove sites with >20% missing data (e.g. -e 'F_MISSING>0.2'). This can be as strict (or lenient) as you want; it's not uncommon to see very conservative filtering at 10% or 5% missing data. However, you can impute missing genotypes to recover -missing data! Harpy can leverage linked-read information to impute genotypes with the +missing data! Harpy can leverage linked-read information to impute genotypes with the impute module. You should try to impute genotypes first before filtering out sites based on missingness.

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