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rebase docs_dev #74

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merged 4 commits into from
Apr 15, 2024
Merged

rebase docs_dev #74

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c5be001
Merge pull request #66 from pdimens/docs_dev
pdimens Apr 3, 2024
b80b141
Merge pull request #67 from pdimens/docs_dev
pdimens Apr 3, 2024
7f67b5e
update
pdimens Apr 11, 2024
144f8bc
update text to reflext api change
pdimens Apr 11, 2024
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12 changes: 7 additions & 5 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,14 @@
test/
src/
.snakemake/
Benchmark/
.Benchmark/
.harpy_envs/
build/
Demultiplex/
Trim/
Variants/
QC/
Align/
SNP/
SV/
Impute/
Phase/
workflows/
rules
workflow/
2 changes: 1 addition & 1 deletion Modules/impute.md
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Expand Up @@ -26,7 +26,7 @@ curate your input VCF to meet criteria 3 and 4 prior to running the `impute` mod
After variants have been called, you may want to impute missing genotypes to get the
most from your data. Harpy uses `STITCH` to impute genotypes, a haplotype-based
method that is linked-read aware. Imputing genotypes requires a variant call file
**containing SNPs**, such as that produced by `harpy variants`. You can impute genotypes with Harpy using the `impute` module:
**containing SNPs**, such as that produced by `harpy snp`. You can impute genotypes with Harpy using the `impute` module:
```bash usage
harpy impute OPTIONS... INPUTS...
```
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2 changes: 1 addition & 1 deletion Modules/phase.md
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Expand Up @@ -16,7 +16,7 @@ order: 2
You may want to phase your genotypes into haplotypes, as haplotypes tend to be more informative
than unphased genotypes (higher polymorphism, captures relationship between genotypes). Phasing
genotypes into haplotypes requires alignment files, such as those produced by `harpy align` and
a variant call file, such as those produced by `harpy variants` or `harpy impute`. **Phasing only
a variant call file, such as those produced by `harpy snp` or `harpy impute`. **Phasing only
works on SNP data**, and will not work for structural variants produced by `LEVIATHAN` or `NAIBR`. You can
phase genotypes into haplotypes with Harpy using the `phase` module:

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