ANNOVAR - column description

Question

[Maxime Lamontagne]

Hi,

I used ANNOVAR to annotate 1000 SNPs for a study.

I've run the table_annovar.pl pipeline in the Quick Start-Up Guide page (http://annovar.openbioinformatics.org/en/latest/user-guide/startup/).

In the output, I do not understand some columns and I can't find this information (pLi, pRec, pNull, P(HI), P(rec)).

Does someone know the meaning of these columns or can direct me somewhere with this information.

Thanks Maxime

Answer 1

[Maxime Lamontagne]

I found the meaning of these columns by downloading a Readme file from ExAC :

The loss-of-function Z score is highly correlated with gene length (r = 0.57). This means that longer genes have higher (more intolerant) scores simply because we are more confident in their predictions. To avoid this correlation, we include the probability of being loss-of-function intolerant (pLI), the suggested metric for evaluating a gene's intolerance (constraint) of loss-of-function variation.

Methods for the creation of pLI will be included in the supplement of the ExAC paper (Lek et al, in prep). Briefly, we used the observed and expected number of loss-of-function variants per gene to determine a posterior probability of each gene belonging to one of three categories: 1) completely tolerant of loss-of-function variation (observed = expected) 2) intolerant of two loss-of-function variants (like recessive genes, observed ~ 0.5expected) 3) intolerant of a single loss-of-function variant (like haploinsufficient genes, observed ~ 0.1expected)

pLI is the probability of falling into category 3, pRec is the probability of falling into category 2, and pNull is the probability of falling into category 1.

[vaish01kv]

GT:AD:AF:F1R2:F2R1:DP:OBC:OBAM:OBAMRC:OBPa:OBParc:OBPsnp:SB:MB  0/1:2,27:0.931:0,16:2,11:29:CAC:.:.:.:1,1,13,14:1,1,14,13

This is the output of annotated vcf of mine using wAnnovar. Can anyone please explain what OBAM, OBAMRC, OBParc, OBPsnp means?

[Shicheng Guo]

What about P(HI)? In addition, there are some other columns without clear information:

[38] "P(HI)"
[39] "HIPred_score"
[40] "HIPred"
[41] "GHIS"
[42] "P(rec)"
[43] "Known_rec_info"
[44] "RVIS_EVS"
[45] "RVIS_percentile_EVS"
[46] "LoF-FDR_ExAC"
[47] "RVIS_ExAC"
[48] "RVIS_percentile_ExAC"
[49] "ExAC_pLI"
[50] "ExAC_pRec"
[51] "ExAC_pNull"
[52] "ExAC_nonTCGA_pLI"
[53] "ExAC_nonTCGA_pRec"
[54] "ExAC_nonTCGA_pNull"
[55] "ExAC_nonpsych_pLI"
[56] "ExAC_nonpsych_pRec"
[57] "ExAC_nonpsych_pNull"
[58] "gnomAD_pLI"
[59] "gnomAD_pRec"
[60] "gnomAD_pNull"
[61] "ExAC_del.score"
[62] "ExAC_dup.score"
[63] "ExAC_cnv.score"
[64] "ExAC_cnv_flag"
[65] "GDI"
[66] "GDI-Phred"
[67] "Gene damage prediction (all disease-causing genes)"
[68] "Gene damage prediction (all Mendelian disease-causing genes)"
[69] "Gene damage prediction (Mendelian AD disease-causing genes)"
[70] "Gene damage prediction (Mendelian AR disease-causing genes)"
[71] "Gene damage prediction (all PID disease-causing genes)"
[72] "Gene damage prediction (PID AD disease-causing genes)"
[73] "Gene damage prediction (PID AR disease-causing genes)"
[74] "Gene damage prediction (all cancer disease-causing genes)"
[75] "Gene damage prediction (cancer recessive disease-causing genes)" [76] "Gene damage prediction (cancer dominant disease-causing genes)" [77] "LoFtool_score"
[78] "SORVA_LOF_MAF0.005_HetOrHom"
[79] "SORVA_LOF_MAF0.005_HomOrCompoundHet"
[80] "SORVA_LOF_MAF0.001_HetOrHom"
[81] "SORVA_LOF_MAF0.001_HomOrCompoundHet"
[82] "SORVA_LOForMissense_MAF0.005_HetOrHom"
[83] "SORVA_LOForMissense_MAF0.005_HomOrCompoundHet"
[84] "SORVA_LOForMissense_MAF0.001_HetOrHom"
[85] "SORVA_LOForMissense_MAF0.001_HomOrCompoundHet"
[86] "Essential_gene"
[87] "Essential_gene_CRISPR"
[88] "Essential_gene_CRISPR2"
[89] "Essential_gene_gene-trap"
[90] "Gene_indispensability_score"
[91] "Gene_indispensability_pred"