#directory to latest cocos_m:
path_to_cocos_m=/storage/cocos_m
#directory to vep:
path_to_vep=/storage/software/ensembl-tools-release-80
${path_to_vep}/scripts/variant_effect_predictor/variant_effect_predictor.pl  -i test.vcf --cache --dir_cache ${path_to_vep}/cache --offline --force_overwrite --dir_plugins path_to_cocos_m --plugin cocos_m -o test.out --stats_text

when using vep version 80, there is a 'negative count' warning. It won't affect the function. This warning has been further removed since version 87.

IMPACT : impact of variant

• high severity if there is a PTC predicted with canonical rules
• mild severity if there is a PTC predicted with noncanonical rules

PTC_POSITION : the new premature codon position in cDNA with variant inserted

TERM_TYPE : termination type of sequence

• PTC,ncanonical,escaping NMD
• PTC,noncanonical,escaping NMD

ALT_AA_SEQ : altered amino acid sequence

1. record exon junction positions
   • get all original exon junction positions
   • insert variant
   • get all modified exon junction positions
2. record truncated cDNA with no 5'UTR but 3'UTR
   • scan the new cDNA and find the new PTC position
3. determine the consequence:
   • if new PTC position doesn't exist: non-stop decayif new PTC position is 55nt early than last exon-exon junction: NMD
   • if new PTC position is early than last exon-exon junction but within 55 nt: escape NMD with canonical rules
   • if there is very long exons (greater than approximately 407nt) inhibit NMD: escape NMD with noncanonical rules
   • if new PTC position is within 150nt from the start codon: escape NMD with noncanonical rules