CADD_summary

IMPORTANT:
-CADD scores for homozygous alleles are not counted twice, just once.
-Multiple entries for one position are discarded, only one is taken into account

Basic usage: python script.py --vep file.vep --tfile tfile --output cadd_sum_output

python script.py -h
usage: script.py [-h] --vep VEP --tfile TFILE [--CADD CADD] [--threshold THRESHOLD] [--gene GENE] [--start_bp START_BP] [--end_bp END_BP] [--denovo DENOVO] --output OUTPUT

[optional] arguments:
-h, --help show this help message and exit
--vep VEP: vep file with CADD scores
--tfile TFILE: Prefix of tped and tfam, both files will be read
[--CADD] CADD_PHRED/CADD_RAW: Either CADD_PHRED or CADD_RAW score will be estimated, default CADD_PHRED
[--threshold] THRESHOLD: CADD threshold, Int
[--gene] GENE_LIST: File with gene list to estimate CADD from
[--start_bp] START_BP: Int with start position in bp
[--end_bp] END_BP: Int with end position in bp
[--denovo] DENOVO: Estimate de novo mutations, WORK IN PROGRESS DO NOT USE
--output OUTPUT output name file