annotate¶
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craft.annotate.annotation_annoVar(df)[source]¶ Use ANNOVAR to annotate prepared internal dataframe.
Describe ANNOVAR functions here.
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craft.annotate.finemap_annotation_annoVar(cred_snps, locus_df)[source]¶ Use ANNOVAR to annotate prepared .cred FINEMAP output.
FINEMAP outputs a .cred space-delimited text file. It contains the 95% credible sets for each causal signal conditional on other causal signals in the genomic region together with conditional posterior inclusion probabilities for each variant.
This function: Filters the locus dataframe (containing all summary statistic information, including chromosome, position, allele 1, allele2), using a list of rsids obtained from the .cred file.
Uses the prepare_df_annoVAR function from craft.annotate to process the new dataframe as ANNOVAR input.
Uses ANNOVAR to add gene-based annotation to the prepared input, using annotate_variation.pl.
Reads the final ANNOVAR input back and returns it as an internal dataframe, removes unnecessary columns, and merges it using rsid as an index to add the posterior probability from the original .cred file.