Is it possible to annotate single genes by snpeff

Question

[misbahabas]

hello

Is it possible to annotate single gene by snpeff ?

anyone have idea about it

[WouterDeCoster]

Like previous threads: EXPLAIN MORE. Give information about what you are doing (MSA of multiple species converted to vcf).

Put some d*mn effort in your questions and don't make this too hard for people trying to help you.

[Titus]

snpeff annotate variant , what do you mean by annotate gene ?

[misbahabas]

I want to annotate variants from genes sequences. I do MSA of one gene in multiple species and convrt into vcf and now want annotate variants from this vcf . I can annotate variants from chr or whole genome but with gene sequence I do not understand how to do it , because snpeff annotate variants chromosome wise

[GenoMax]

I do MSA of one gene in multiple species and convrt into vcf and now want annotate variants from this vcf.

What exactly are you trying to do? Generally SNP discovery is done for a single species.

[misbahabas]

I am trying to annotate vcf which contain position of genes instead of genome. after multiple sequence alignment I used snp-sites to convert fast into vcf which contain snp position in genes Like

    ##fileformat=VCFv4.1
    ##INFO=<ID=AB,Number=1,Type=String,Description="Alt Base">
    #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  MP-Hsap_AM  MP-Lafr_AM  MP-Cang_AM  MP-Ptro_AM  MA-Phod_AM  MP-Pcoq_AM  MC-Clup_AM  MC-Fcat_AM  MA-Chir_AM  MR-Mmus_AM  MR-Jjac_AM  MR-Hgla_AM  MC-Mnat_AM  MH-Nleu_AM  MC-Oros_AM  MA-Sscr_AM  MP-Ppan_AM  MP-Mmul_AM  MA-Oari_AM  MA-Etel_AM  MC-Ptig_AM  AA-Xtro_AM  MA-Bbub_AM  MC-Lwed_AM  MP-Ggor_AM  MA-Bmut_AM  MA-Bind_AM  
    1   2   .   -   T,A .   .   AB  .   .   .   T   .   .   .   .   A   .   .   .   A   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
    1   4   .   -   T,G .   .   AB  .   .   .   T   .   .   .   .   .   .   .   .   G   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
    1   5   .   -   T,A .   .   AB  .   .   .   T   .   .   .   .   .   .   .   .   A   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
    1   6   .   -   G,T .   .   AB  .   .   .   G   .   .   .   .   .   .   .   .   T   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
    1   8   .   -   G,A .   .   AB  .   .   .
1   22018   .   G   A,C .   .   AB  .   .   .   .   .   .   .   .   .   .   .   .   A   .   .   .   .   .   .   .   .   C   .   .   .   .   .   .
1   22019   .   T   G   .   .   AB  .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .

Now i should annotate these variants using snpeff and variant effect predictor , to find misssense variants, but I cannot understand how to do it because its a gene sequence and vcf file contain gene position not genome position

[misbahabas]

Is it possible to annotate vcf which contain gene positions in different species by snpeff?

[Titus]

I don t think you can you need genomic position , and i m not sure MSA work

[misbahabas]

there is any other tool which take gene positions(not genomic positions) as a input in vcf format, to do annotation of gene variants ??

[Titus]

I never heard about this kind of tool. In your example where is the gene name/ID information for example ? How the tool can guess the gene name to translate the mutation consequences ?

By the way I m not sure you are using the good "pipeline"/algorithm to find a solution to your question.

[misbahabas]

i also try this

##fileformat=VCFv4.1
##INFO=<ID=AB,Number=1,Type=String,Description="Alt Base">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  MP-Hsap_AM  MP-Lafr_AM  MP-Cang_AM  MP-Ptro_AM  MA-Phod_AM  MP-Pcoq_AM  MC-Clup_AM  MC-Fcat_AM  MA-Chir_AM  MR-Mmus_AM  MR-Jjac_AM  MR-Hgla_AM  MC-Mnat_AM  MH-Nleu_AM  MC-Oros_AM  MA-Sscr_AM  MP-Ppan_AM  MP-Mmul_AM  MA-Oari_AM  MA-Etel_AM  MC-Ptig_AM  AA-Xtro_AM  MA-Bbub_AM  MC-Lwed_AM  MP-Ggor_AM  MA-Bmut_AM  MA-Bind_AM  
1   2   gene2206    -   T,A .   .   AB  .   .   .   T   .   .   .   .   A   .   .   .   A   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   4   gene2206    -   T,G .   .   AB  .   .   .   T   .   .   .   .   .   .   .   .   G   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   5   gene2206    -   T,A .   .   AB  .   .   .   T   .   .   .   .   .   .   .   .   A   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   6   gene2206    -   G,T .   .   AB  .   .   .   G   .   .   .   .   .   .   .   .   T   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   8   gene2206    -   G,A .   .   AB  .   .   .   G   .   .   .   .   .   .   .   .   A   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .

but Its not usefull, results remain same, tool considered chromosomes position not gene positon

output like this

##fileformat=VCFv4.1
##INFO=<ID=AB,Number=1,Type=String,Description="Alt Base">
##SnpEffVersion="4.3p (build 2017-06-06 09:55), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh38.p7.RefSeq test_chr_gene.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  MP-Hsap_AM  MP-Lafr_AM  MP-Cang_AM  MP-Ptro_AM  MA-Phod_AM  MP-Pcoq_AM  MC-Clup_AM  MC-Fcat_AM  MA-Chir_AM  MR-Mmus_AM  MR-Jjac_AM  MR-Hgla_AM  MC-Mnat_AM  MH-Nleu_AM  MC-Oros_AM  MA-Sscr_AM  MP-Ppan_AM  MP-Mmul_AM  MA-Oari_AM  MA-Etel_AM  MC-Ptig_AM  AA-Xtro_AM  MA-Bbub_AM  MC-Lwed_AM  MP-Ggor_AM  MA-Bmut_AM  MA-Bind_AM  
1   2   gene2206    -   T,A .   .   AB;ANN=T|intergenic_region|MODIFIER|CHR_START-DDX11L1|CHR_START-DDX11L1|intergenic_region|CHR_START-DDX11L1|||n.2->T||||||,A|intergenic_region|MODIFIER|CHR_START-DDX11L1|CHR_START-DDX11L1|intergenic_region|CHR_START-DDX11L1|||n.2->A||||||  .   .   .   T   .   .   .   .   A   .   .   .   A   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   4   gene2206    -   T,G .   .   AB;ANN=T|intergenic_region|MODIFIER|CHR_START-DDX11L1|CHR_START-DDX11L1|intergenic_region|CHR_START-DDX11L1|||n.4->T||||||,G|intergenic_region|MODIFIER|CHR_START-DDX11L1|CHR_START-DDX11L1|intergenic_region|CHR_START-DDX11L1|||n.4->G||||||  .   .   .   T   .   .   .   .   .   .   .   .   G   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   5   gene2206    -   T,A .   .   AB;ANN=T|intergenic_region|MODIFIER|CHR_START-DDX11L1|CHR_START-DDX11L1|intergenic_region|CHR_START-DDX11L1|||n.5->T||||||,A|intergenic_region|MODIFIER|CHR_START-DDX11L1|CHR_START-DDX11L1|intergenic_region

This output same as when gene id/name not used. its not effect the output How can i confirm its true or false

[misbahabas]

is there any way to convert gene positions into genomic positions ?

[Titus]

First of all i think you should read what you are writing because you can t explain you problem in 1 line !
What is MSA ? (you too lazy to write it completely and i m an ignorant )

If i understood a peace of what you saying you tried to annotate a vcf which got gene position instead of genomic position ?

[GenoMax]

MSA = Multiple Sequence Alignment.

[misbahabas]

MSA = Multiple Sequence Alignment.

yes i want to annotate a vcf which got gene position instead of genomic position ?