INDELs VEP anntotation Consequence is missense_variant

[pl618]

pTuneos/src/core/VariantCallingFormat/VCFprocessor.py

Line 72 in e6cfd0e

cmd_vep_indel=vep_path + " -i " + somatic_out_fold + '/' + prefix + '_'+ 'INDELs_only.recode.vcf' + " --cache --dir " + vep_cache_path + " --dir_cache " + vep_cache_path + " --force_overwrite --canonical --symbol -o STDOUT --offline | filter_vep --ontology --filter \"Consequence is missense_variant\" -o " + somatic_out_fold + '/' + prefix + '_'+ 'mutect_indel_vep_ann.txt' + " --force_overwrite"

For INDELs, it seems that no Consequence is missense_variant ?

[renyongzhe]

pTuneos/src/core/VariantCallingFormat/VCFprocessor.py

Line 72 in e6cfd0e

cmd_vep_indel=vep_path + " -i " + somatic_out_fold + '/' + prefix + '_'+ 'INDELs_only.recode.vcf' + " --cache --dir " + vep_cache_path + " --dir_cache " + vep_cache_path + " --force_overwrite --canonical --symbol -o STDOUT --offline | filter_vep --ontology --filter \"Consequence is missense_variant\" -o " + somatic_out_fold + '/' + prefix + '_'+ 'mutect_indel_vep_ann.txt' + " --force_overwrite"

For INDELs, it seems that no Consequence is missense_variant ?

I think so. The Consequence is always frameshift or some else.

[ChiZhou-SITI]

Hi, all
You both are right!

Actually, Consequence for INDEL should be "coding_sequence_variant" and in the VEP annotation results, it might be "frameshift_variant" or "inframe_deletion" or something orther.
We have modified it and test it in several datasets.
Thank you for your feedback.

Best，
Chi