Add documentation for the de-novo pipeline #675
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mwalker174
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Sep 11, 2024
| slug: denovo | ||
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| The de-novo workflow operates on the annotated multi-sample VCF file created by |
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| The de-novo workflow operates on the annotated multi-sample VCF file created by | |
| The de novo SV workflow operates on the annotated multi-sample VCF file created by |
| ### Inputs | ||
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| - `vcf_file`: output of [AnnotateVcf](./av) called output_vcf. | ||
| Note thatAll families in the vcf file must be included in the pedigree file |
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| Note thatAll families in the vcf file must be included in the pedigree file | |
| Note that all families in the vcf file must be included in the pedigree file |
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| - `ped_input`: Must have a header as follows: | ||
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| | FamID | IndividualID | FatherID | MotherID | Gender | Affected | | ||
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Better to just link to this page: https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format
| | FamID | IndividualID | FatherID | MotherID | Gender | Affected | | ||
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| - `genomic_disorder_input`: a file in BED format that contains regions of genomic disorder; |
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| - `genomic_disorder_input`: a file in BED format that contains regions of genomic disorder; | |
| - `genomic_disorder_input`: a file in BED format that contains genomic disorder regions; |
| - `genomic_disorder_input`: a file in BED format that contains regions of genomic disorder; | ||
| variants that overlap these regions will not be removed from the input VCF file. | ||
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| - `contigs`: Should be set to the following list. |
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| - `contigs`: Should be set to the following list. | |
| - `contigs`: List of reference contig names, e.g. for `hg38`: |
| [ "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX" ]` | ||
| ``` | ||
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| - `python_config`: a text file as the following. |
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| - `python_config`: a text file as the following. | |
| - `python_config`: a text file defining the following parameters: |
| gq_min: '0' | ||
| ``` | ||
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| Note that you value may increase the value of `cohort_AF` if the cohort is small. |
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| a txt file with first column as batch and second column raw file generated from | ||
| module05-ClusterBatch for all callers except depth (clustered_manta_vcf, clustered_melt_vcf, clustered_wham_vcf). |
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| a txt file with first column as batch and second column raw file generated from | |
| module05-ClusterBatch for all callers except depth (clustered_manta_vcf, clustered_melt_vcf, clustered_wham_vcf). | |
| a txt file where the first column is the batch name and second column is the raw file generated from | |
| the ClusterBatch workflow for all callers except depth (clustered_manta_vcf, clustered_melt_vcf, clustered_wham_vcf). |
| - Must match batch names in batch_bincov, batch_raw_file, and batch_depth_raw_file | ||
| - These batches and the samples contained in them are relevant in regards to the bincov matrices and raw files | ||
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| - `prefix`: choose any prefix which will become the prefix of output files |
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| - `prefix`: choose any prefix which will become the prefix of output files | |
| - `prefix`: a prefix for output filenames |
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This file is a lot of detail. IMO, it would be better to reference the scripts themselves and have those be sufficiently organized/commented that the methods are clear.
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Thank you, @mwalker174, for the feedback! I agree that we need the setup of the inputs polished before we add docs; I will update docs after the inputs are updated. |
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This PR extends the docs in the following areas: