Tips

How to configure ANNOTATION_KEY_CONFIG yaml file

The ANNOTATION_KEY_CONFIG yaml file contains functional_score and functional_annotation. Each file is in bed format and should be written with their short name that represents them. This name will be further used in other analyses.

When setting the short name, avoid using underscores (‘_’). Underscores are used to distinguish different domains within a single category. For example, a category ‘A_B_C_D_E’ will be recognized as five domains, but if the name of the category is ‘A_B_C_D_E_F’, it will cause error while association testing, as the category is divided into six domains.

An example for ANNOTATION_KEY_CONFIG yaml file looks like below.

functional_score:
  bed1.bed.gz: annot1
  bed2.bed.gz: annot2
functional_annotation:
  bed3.bed.gz: annot_3 # Do not use underscores like this. Users can use 'annot3' instead.
  bed4.bed.gz: annot4

The files should be located inside ANNOTATION_DATA_DIR. For preparation step, these files should be indexed using tabix.

As an example, users can sort and index their bed file like below.

cat bed1.bed | sort -k1,1V -k2,2n -k3,3n -t$'\t' | bgzip -c > sorted.bed1.bed.gz
tabix -p bed sorted.bed1.bed.gz

How to add or remove a gene set

Modify the txt file used for gene set (GENE_MATRIX).

The gene set contains gene ID, gene name and columns that represents each set of genes. To add or remove gene sets, users can add or remove columns.

gene_id	gene_name	ProteinCoding	lincRNA	ASDTADAFDR03
ENSG00000000003.15	TSPAN6	1	0	0
ENSG00000000005.6	TNMD	1	0	0
ENSG00000000419.14	DPM1	1	0	0

Then, configure again.

cwas configuration -f

If users already have the annotated VCF (*annotated.vcf.gz) and gene set is the only thing they changed, then they can start from categorization step. Gene sets are first used in the categorization step.

How to add or remove a functional annotation or score

Modify the ANNOTATION_KEY_CONFIG yaml file. Add a new line or remove previous lines from the file.

Then, configure again.

cwas configuration -f

The annotation of CWAS-Plus contains two steps: (1) VEP annotation, (2) BED custom annotation. If the output of each step already exists, then the step is skipped.

If users already have the VEP annotated file (*.vep.vcf.gz), they can start from annotation step.

CWAS-Plus skips VEP annotation if the VEP annotated file already exists.

cwas annotation -v INPUT.vcf -o_dir OUTPUT_DIR -p 8

However, before annotation, please remove the annotated VCF (*annotated.vcf.gz). If the annotated VCF exists, CWAS-Plus will also skip BED custom annotation step.