How to Add FORMAT column from VCF file to table?

Question

[windsur]

Hello! I am new using vep annotation and I have seen a lot of questions in how to include AD:DP (info fields) in --tab format. But I did not find the answer :(

I have used vep to annotated my VCF files using --tab and --vcf arguments separately. So I have 2 files (one tab delimited without the INFO fields and the other one is the VCF with the INFO fields).

I was wondering how can I add these fields from the VCF file to the one that is tab delimited.

The VCF file with the FORMAT field GT:GQ:AD:DP:VF:NL:SB:NC that I need:

> #CHROM    POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  L30-1_S1.bam
chr2    208245343   .   T   C   0   q30 DP=894;phyloP=0.159;CSQ=C|missense_variant|MODERATE|IDH1|ENSG00000138413|Transcript|ENST00000345146|protein_coding|5/10||ENST00000345146.7:c.496A>G|ENSP00000260985.2:p.Thr166Ala|719|496|166|T/A|Aca/Gca|||-1||SNV|HGNC|HGNC:5382|YES|NM_005896.4||1|P1|CCDS2381.1|ENSP00000260985|O75874.215|A0A024R3Y6.7|UPI000012D1B4||1|tolerated_low_confidence(0.13)|benign(0.001)|PDB-ENSP_mappings:1t09.A&PDB-ENSP_mappings:1t09.B&PDB-ENSP_mappings:1t0l.A&PDB-ENSP_mappings:1t0l.B&PDB-ENSP_mappings:6vg0.C&PANTHER:PTHR11822&PANTHER:PTHR11822:SF28&TIGRFAM:TIGR00127&Gene3D:3.40.718.10&PIRSF:PIRSF000108&Pfam:PF00180&SMART:SM01329&Superfamily:SSF53659||||||||||||||||||||||||||||||||MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL    GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:891,3:894:0.003356:18:-11.0619:0.0366
chr2    208245401   .   A   G   0   q30 DP=683;phyloP=0.159;CSQ=G|synonymous_variant|LOW|IDH1|ENSG00000138413|Transcript|ENST00000345146|protein_coding|5/10||ENST00000345146.7:c.438T>C|ENSP00000260985.2:p.Val146%3D|661|438|146|V|gtT/gtC|||-1||SNV|HGNC|HGNC:5382|YES|NM_005896.4||1|P1|CCDS2381.1|ENSP00000260985|O75874.215|A0A024R3Y6.7|UPI000012D1B4||1|||PDB-ENSP_mappings:1t09.A&PDB-ENSP_mappings:1t09.B&PDB-ENSP_mappings:1t0l.A&PDB-ENSP_mappings:1t0l.B&PDB-ENSP_mappings:1t0l.C&PDB-ENSP_mappings:1t0l.D&PDB-ENSP_mappings:6vei.A&PDB-ENSP_mappings:6vei.B&PDB-ENSP_mappings:6vg0.A&PDB-ENSP_mappings:6vg0.B&PDB-ENSP_mappings:6vg0.C&PANTHER:PTHR11822&PANTHER:PTHR11822:SF28&TIGRFAM:TIGR00127&Gene3D:3.40.718.10&PIRSF:PIRSF000108&Pfam:PF00180&SMART:SM01329&Superfamily:SSF53659||||||||||||||||||||||||||||||||MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL  GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:681,2:683:0.002928:18:-12.0263:0.0243
chr2    208245402   .   A   G   0   q30 DP=686;phyloP=0.178;CSQ=G|missense_variant|MODERATE|IDH1|ENSG00000138413|Transcript|ENST00000345146|protein_coding|5/10||ENST00000345146.7:c.437T>C|ENSP00000260985.2:p.Val146Ala|660|437|146|V/A|gTt/gCt|||-1||SNV|HGNC|HGNC:5382|YES|NM_005896.4||1|P1|CCDS2381.1|ENSP00000260985|O75874.215|A0A024R3Y6.7|UPI000012D1B4||1|tolerated_low_confidence(0.16)|possibly_damaging(0.823)|PDB-ENSP_mappings:1t09.A&PDB-ENSP_mappings:1t09.B&PDB-ENSP_mappings:1t0l.A&PDB-ENSP_mappings:1t0l.B&PDB-ENSP_mappings:6vg0.A&PDB-ENSP_mappings:6vg0.B&PDB-ENSP_mappings:6vg0.C&PANTHER:PTHR11822&PANTHER:PTHR11822:SF28&TIGRFAM:TIGR00127&Gene3D:3.40.718.10&PIRSF:PIRSF000108&Pfam:PF00180&SMART:SM01329&Superfamily:SSF53659||||||||||||||||||||||||||||||||MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL   GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:684,2:686:0.002915:18:-12.0416:0.0200
chr2    208245451   .   GA  G   100 R3x6    DP=666;CSQ=-|intron_variant|MODIFIER|IDH1|ENSG00000138413|Transcript|ENST00000345146|protein_coding||4/9|ENST00000345146.7:c.415-28del|||||||rs569424950||-1||deletion|HGNC|HGNC:5382|YES|NM_005896.4||1|P1|CCDS2381.1|ENSP00000260985|O75874.215|A0A024R3Y6.7|UPI000012D1B4||1||||||||||||0.01454|0.01345|0.002208|0.002132|0.001866|0.002006|0.002225|0.00063|0.002518|0.001787|0.002821|0.01454|AA|||||||||||MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL  GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:619,47:666:0.070571:37:-100.0000:0.0000

The VCF tab:

#Uploaded_variation Location    Allele  Gene    Feature Feature_type    Consequence cDNA_position   CDS_position    Protein_position    Amino_acids Codons  Existing_variation  IMPACT  DISTANCE    STRAND  FLAGS   VARIANT_CLASS   SYMBOL  SYMBOL_SOURCE   HGNC_ID BIOTYPE CANONICAL   MANE_SELECT MANE_PLUS_CLINICAL  TSL APPRIS  CCDS    ENSP    SWISSPROT   TREMBL  UNIPARC UNIPROT_ISOFORM GENE_PHENO  SIFT    PolyPhen    EXON    INTRON  DOMAINS miRNA   HGVSc   HGVSp   HGVS_OFFSET AF  AFR_AF  AMR_AF  EAS_AF  EUR_AF  SAS_AF  AA_AF   EA_AF   gnomAD_AF   gnomAD_AFR_AF   gnomAD_AMR_AF   gnomAD_ASJ_AF   gnomAD_EAS_AF   gnomAD_FIN_AF   gnomAD_NFE_AF   gnomAD_OTH_AF   gnomAD_SAS_AF   MAX_AF  MAX_AF_POPS CLIN_SIG    SOMATIC PHENO   PUBMED  MOTIF_NAME  MOTIF_POS   HIGH_INF_POS    MOTIF_SCORE_CHANGE  TRANSCRIPTION_FACTORS   FrameshiftSequence  WildtypeProtein
chr2_208245343_T/C  chr2:208245343  C   ENSG00000138413 ENST00000345146 Transcript  missense_variant    719 496 166 T/A Aca/Gca -   MODERATE    -   -1  -   SNV IDH1    HGNC    HGNC:5382   protein_coding  YES NM_005896.4 -   1   P1  CCDS2381.1  ENSP00000260985 O75874.215  A0A024R3Y6.7    UPI000012D1B4   -   1   tolerated_low_confidence(0.13)  benign(0.001)   5/10    -   PDB-ENSP_mappings:1t09.A,PDB-ENSP_mappings:1t09.B,PDB-ENSP_mappings:1t0l.A,PDB-ENSP_mappings:1t0l.B,PDB-ENSP_mappings:1t0l.C,PDB-ENSP_mappings:1t0l.D,PDB-ENSP_mappings:3inm.A,PDB-ENSP_mappings:6vei.B,PDB-ENSP_mappings:6vg0.A,PDB-ENSP_mappings:6vg0.B,PDB-ENSP_mappings:6vg0.C,PANTHER:PTHR11822,PANTHER:PTHR11822:SF28,TIGRFAM:TIGR00127,Gene3D:3.40.718.10,PIRSF:PIRSF000108,Pfam:PF00180,SMART:SM01329,Superfamily:SSF53659  -   ENST00000345146.7:c.496A>G  ENSP00000260985.2:p.Thr166Ala   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
chr2_208245401_A/G  chr2:208245401  G   ENSG00000138413 ENST00000345146 Transcript  synonymous_variant  661 438 146 V   gtT/gtC -   LOW -   -1  -   SNV IDH1    HGNC    HGNC:5382   protein_coding  YES NM_005896.4 -   1   P1  CCDS2381.1  ENSP00000260985 O75874.215  A0A024R3Y6.7    UPI000012D1B4   -   1   -   -   5/10    -   PDB-ENSP_mappings:1t09.A,PDB-ENSP_mappings:1t09.B,PDB-ENSP_mappings:1t0l.A,PDB-ENSP_mappings:1t0l.B,PDB-ENSP_mappings:6vg0.A,PDB-ENSP_mappings:6vg0.B,PDB-ENSP_mappings:6vg0.C,PANTHER:PTHR11822,PANTHER:PTHR11822:SF28,TIGRFAM:TIGR00127,Gene3D:3.40.718.10,PIRSF:PIRSF000108,Pfam:PF00180,SMART:SM01329,Superfamily:SSF53659  -   ENST00000345146.7:c.438T>C  ENSP00000260985.2:p.Val146%3D   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
chr2_208245402_A/G  chr2:208245402  G   ENSG00000138413 ENST00000345146 Transcript  missense_variant    660 437 146 V/A gTt/gCt -   MODERATE    -   -1  -   SNV IDH1    HGNC    HGNC:5382   protein_coding  YES NM_005896.4 -   1   P1  CCDS2381.1  ENSP00000260985 O75874.215  A0A024R3Y6.7    UPI000012D1B4   -   1   tolerated_low_confidence(0.16)  possibly_damaging(0.823)    5/10    -   PDB-ENSP_mappings:1t09.A,PDB-ENSP_mappings:1t09.B,PDB-ENSP_mappings:1t0l.A,PDB-ENSP_mappings:1t0l.B,PDB-ENSP_mappings:1t0l.C,PDB-ENSP_mappings:1t0l.D,PDB-ENSP_mappings:3inm.A,PDB-ENSP_mappings:6vei.B,PDB-ENSP_mappings:6vg0.A,PDB-ENSP_mappings:6vg0.B,PDB-ENSP_mappings:6vg0.C,PANTHER:PTHR11822,PANTHER:PTHR11822:SF28,TIGRFAM:TIGR00127,Gene3D:3.40.718.10,PIRSF:PIRSF000108,Pfam:PF00180,SMART:SM01329,Superfamily:SSF53659  -   ENST00000345146.7:c.437T>C  ENSP00000260985.2:p.Val146Ala   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL
chr2_208245452_A/-  chr2:208245452  -   ENSG00000138413 ENST00000345146 Transcript  intron_variant  -   -   -   -   -   rs569424950 MODIFIER    -   -1  -   deletion    IDH1    HGNC    HGNC:5382   protein_coding  YES NM_005896.4 -   1   P1  CCDS2381.1  ENSP00000260985 O75874.215  A0A024R3Y6.7    UPI000012D1B4   -   1   -   -   -   4/9 -   -   ENST00000345146.7:c.415-28del   -   -   -   -   -   -   -   -   0.01454 0.01345 0.002208    0.002132    0.001866    0.002006    0.002225    0.00063 0.002518    0.001787    0.002821    0.01454 AA  -   -   -   -   -   -   -   -   -   -   MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL

It will be very helpfull if someone could give me some light. I have omitted all the commented rows from the VCF files. Is there any VEP plugin that can retain the original columns of the VCF file?

Thanks!!

[Pierre Lindenbaum]

if you have all the needed information in the VCF output, why would you need to join it with the tab file ?

[windsur]

Yes, but is to avoid to rewrite all the headers. And also (the main reason) is because the tab format is easier to visualize the data in excel for my co-workers.

[Sanya]

Hey I really need your help regarding vcf file . Please can you help me

Answer 1

[Emily]

If you get your output as VCF it will retain all the original input from your VCF. Alternatively, you can use the custom option specifying your same input file and the fields you want to include.

[windsur]

Thanks @Emily_Ensembl , but I am not sure how to create a custom field. Could you provide me an example of this case? thanks

[Emily]

There's an example listed under ClinVar on that documentation page.