Using VEP custom input

Question

[Sd]

I have a DataFrame with the following columns. Is there any way to use this file in VEP to include columns 6 to 12 in my variant annotation outputs?

    chr   start     end       transcript    gene   exp_snv  obs_snv      pLI      o/e  lof.oe_ci_lower  lof.oe_ci.upper         biotype  canonical  mane_select
0  chr1   65419   71585  ENST00000641515   OR4F5   0.53873      0.0  0.33668  0.00000        0.000            1.828  protein_coding       True         True
1  chr1  923923  944574  ENST00000616016  SAMD11  54.47500     75.0  0.00000  1.37680        1.204            1.764  protein_coding       True         True
2  chr1  923923  944574  ENST00000618323  SAMD11  54.13100     76.0  0.00000  1.40400        1.231            1.795  protein_coding      False        False
3  chr1  925150  935793  ENST00000437963  SAMD11  15.47900     15.0  0.00001  0.96906        0.483            1.272  protein_coding      False        False
4  chr1  925731  944574  ENST00000342066  SAMD11  55.24600     75.0  0.00000  1.35760        1.141            1.693  protein_coding      False        False

[Sd]

Initially, I converted the file to GFF3 format in order to run VEP, but I got warnings and couldn’t figure out what the problem was.

GFF3 format file which created to use ./vep --custom or --gff:

chr1    gnomAD.v4.1_constraint  transcript      65419   71585   .       +       .       ID=ENST00000641515;Name=OR4F5;Parent=OR4F5;exp_snv=0.53873;obs_snv=0.00000;pLI=0.33668;o/e=0.00000;lof.oe_ci_lower=0.0;lof.oe_ci.upper=1.828;biotype=protein_coding;canonical=True;mane_select=True
chr1    gnomAD.v4.1_constraint  transcript      923923  944574  .       +       .       ID=ENST00000616016;Name=SAMD11;Parent=SAMD11;exp_snv=54.47500;obs_snv=75.00000;pLI=0.00000;o/e=1.37680;lof.oe_ci_lower=1.204;lof.oe_ci.upper=1.764;biotype=protein_coding;canonical=True;mane_select=True
chr1    gnomAD.v4.1_constraint  transcript      923923  944574  .       +       .       ID=ENST00000618323;Name=SAMD11;Parent=SAMD11;exp_snv=54.13100;obs_snv=76.00000;pLI=0.00000;o/e=1.40400;lof.e_ci_lower=1.231;lof.oe_ci.upper=1.795;biotype=protein_coding;canonical=False;mane_select=False
chr1    gnomAD.v4.1_constraint  transcript      925150  935793  .       +       .       ID=ENST00000437963;Name=SAMD11;Parent=SAMD11;exp_snv=15.47900;obs_snv=15.00000;pLI=0.00001;lof.o/e=0.96906;oe_ci_lower=0.483;lof.oe_ci.upper=1.272;biotype=protein_coding;canonical=False;mane_select=False

But I am getting the following warnings like this:

WARNING: Parent entries with the following IDs were not found or skipped due to invalid types: TBX1, GSC2, TSSK2, HIRA, DGCR2, CLDN5, GP1BB, SEPTIN5, nan, UFD1, TXNRD2, COMT, CDC45, ESS2, C22orf39, ARVCF, MRPL40, CLTCL1, SLC25A1, RTL10, GNB1L
WARNING: 167 : WARNING: Parent entries with the following IDs were not found or skipped due to invalid types: CLTCL1, SLC25A1, MRPL40, RTL10, GNB1L, UFD1, nan, ESS2, C22orf39, ARVCF, COMT, TXNRD2, CDC45, SEPTIN5, HIRA, TSSK2, TBX1, GSC2, GP1BB, CLDN5, DGCR2
WARNING: Parent entries with the following IDs were not found or skipped due to invalid types: CLTCL1, SLC25A1, MRPL40, RTL10, GNB1L, UFD1, nan, ESS2, C22orf39, ARVCF, COMT, TXNRD2, CDC45, SEPTIN5, HIRA, TSSK2, TBX1, GSC2, GP1BB, CLDN5, DGCR2
WARNING: 218 : WARNING: Parent entries with the following IDs were not found or skipped due to invalid types: THAP7, SCARF2, MED15, DGCR8, PI4KA, COMT, TXNRD2, CCDC188, ZDHHC8, SERPIND1, KLHL22, AIFM3, RANBP1, RTN4R, LZTR1, CRKL, TANGO2, ZNF74, ARVCF, SNAP29, nan, DGCR6L, TRMT2A, USP41
WARNING: Parent entries with the following IDs were not found or skipped due to invalid types: THAP7, SCARF2, MED15, DGCR8, PI4KA, COMT, TXNRD2, CCDC188, ZDHHC8, SERPIND1, KLHL22, AIFM3, RANBP1, RTN4R, LZTR1, CRKL, TANGO2, ZNF74, ARVCF, SNAP29, nan, DGCR6L, TRMT2A, USP41

Do you have any thoughts on this? Which format should I use to avoid the following warnings?

Answer 1

[Pierre Lindenbaum]

VEP can integrate custom annotation from standard format files into your results by using the --custom flag.

see https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html

( but I would just index the file with tabix and use bcftools annotate )