VEP annotation question
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Entering edit mode
4 months ago

hi, everyone:

i meet a question like this :

chr8 145742514 . A G 123 PASS NS=1;DP=52;AF=0.5 GT:GQ:DP:HQ 1/1:48:52:51,51

chr8 145742515 . C A 123 PASS NS=1;DP=52;AF=0.5 GT:GQ:DP:HQ 1/1:48:52:51,51

my vep commands:

/jdfstj1/B2C_COM_P1/5_Personal/lmt/software/VEP/ensembl-vep-release-104/ensembl-vep-release-104/vep \
--fork 4 \
--assembly GRCh37 \
--offline \
--cache \
--dir_cache /jdfstj1/B2C_COM_P1/Clinical_product/7_tj_ycb/vep_update_database_lmt \
--refseq  \
--use_transcript_ref \
--exclude_predicted \
--fasta /jdfstj1/B2C_COM_P1/Clinical_product/7_tj_ycb/vep_update_database_lmt/hg19/hg19.fa  \
-i tmp.vcf  \
--vcf_info_field ANN \
--force_overwrite \
--tab \
-o tmp104t.out  \
--verbose \
--no_escape  \
--everything \

my result as follow: enter image description here

the 'BAM_EDIT' column is empty。

i test vep95.5 with the same vcf

vep  \
--cache \
--dir_cache /jdfstj1/B2C_COM_P1/pipeline/Lung_T/OsmartT/database/vep_cache \
--assembly GRCh37 \
--use_transcript_ref \
--offline --refseq --everything --exclude_predicted \
--fasta /jdfstj1/B2C_COM_P1/pipeline/Lung_T/OsmartT/database/vep_cache/hg19/hg19.fa \
--format vcf \
--vcf_info_field ANN \
--force_overwrite \
--tab \
--verbose \
--no_escape \
-i tmp.vcf \
-o tmp.94.out  \
--everything  \

the result of vep95.5 like follow: enter image description here

the 'BAM_EDIT' column in VEP95.5 is normal

question:

nowadays, i am using vep104. and i want to use the options --use_transcript_ref, how to solve the ‘BAM_EDIT’ bug.

use_transcript_ref BAM_EDIT VEP • 198 views
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Tagging: Ben_Ensembl

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