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add sample annotation docs
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@AtaJadidAhari
AtaJadidAhari committed Oct 7, 2024
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Expand Up @@ -169,7 +169,7 @@ Calling variants on RNA-seq data may be useful for researchers who do not have a
The RNA variant calling process uses information from multiple samples (as designated by the ``groups`` variable) to improve the quality of the called variants. However, the larger the group size, the more costly the computation is in terms of time and resources. To prioritize accuracy, include many samples in each ``DROP_GROUP``, and to prioritize speed up computation, separate samples into many groups. Additionally, certain vcf and bed files must be included to further boost the quality of the called variants (refer to `files-to-download`_).

===================== ========= ================================================================================================================================================================================================ =========
Parameter Type Description Default/Examples
Parameter Type Description Default/Examples
===================== ========= ================================================================================================================================================================================================ =========
run boolean If true, the module will be run. If false, it will be ignored. ``true``
groups list Same as in aberrant expression. ``# see aberrant expression example``
Expand Down Expand Up @@ -226,6 +226,34 @@ column order does not matter. Also, it does not matter where it is stored, as th
specified in the config file. Here we provide some examples on how to deal with certain
situations. For simplicity, we do not include all possible columns in the examples.

===================== ========= ================================================================================================================================================================================================ ==========================
Parameter Type Description Default/Examples
===================== ========= ================================================================================================================================================================================================ ==========================
RNA_ID character Unique identifier from an RNA assay. ``sample1``
RNA_BAM_FILE character Absolute path of the BAM file derived from RNA-seq. A BAM file can belong to only one RNA_ID and vice versa. ``path/to/sample1.bam``
DNA_VCF_FILE character Absolute path to the corresponding VCF. The DNA_ID has to match the ID inside the VCF file. In case a multisample VCF is used, write the file name for each sample. ``path/to/sample1.vcf``
DNA_ID character Unique identifier from a DNA assay. ``sample1``
DROP_GROUP list The analysis group(s) that the RNA assay belongs to. Multiple groups must be separated by commas and no spaces (e.g. blood,WES,groupA). We recommend doing a different analysis for each tissue
as gene expression and splicing can be tissue specific. ``group1,group2``
PAIRED_END boolean Either TRUE or FALSE, depending on whether the sample comes from paired-end RNA-seq or not. ``TRUE``
COUNT_MODE character Either ``Union``, ``IntersectionStrict`` or ``IntersectionNotEmpty``. Refer to the documentation of HTSeq for details. ``IntersectionStrict``
COUNT_OVERLAPS character Either TRUE or FALSE, depending on whether reads overlapping different regions are allowed and counted. ``TRUE``
STRAND character Either yes, no, or reverse: ``no`` means that the sequencing was not strand specific; ``yes`` that it was strand specific, and the first read in the pair is on the same strand as the feature
and the second read on the opposite strand; and ``reverse`` that the sequencing is strand specific and the first read in the pair is on the opposite strand to the feature and the second read
on the same strand. ``no``
HPO_TERMS list Comma-separated phenotypes encoded as HPO terms. ``HP:0001479, HP:0005591``
GENE_COUNTS_FILE character (Only required for aberrant expression external samples) Location of external gene-level count matrix. ``/path/to/gene_counts/``
GENE_ANNOTATION character (Only required for aberrant expression external samples) Gene annotation used to obtain the count matrix. Must correspond to the key of an entry in the geneAnnotation parameter of the config
file. ``v29``
GENOME character (Optional) Either ``ncbi`` or ``ucsc`` indicating the reference genome assembly. ``ncbi``
SPLICE_COUNTS_DIR character (Only required for aberrant splicing external samples) Location of external files required for aberrant splicing module as explained above. ``/path/to/splicing_dir/``
SEX character (Optional) Either ``m``, ``male``, ``f`` or ``female`` or ``unknown`` . When provided, sex matching algorithm will be run to match provided sex values to bam files and predict SEX value for
unknown samples. ``m``
TISSUE character (Optional) ``BRAIN``
DISEASE character (Optional) ``AML``
===================== ========= ================================================================================================================================================================================================ ==========================



Using External Counts
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