Output Options

VCF-like output

With –gseq transvar appends genomic sequence information as additional columns with pos, ref, alt following the VCF convention (i.e., indels are left-aligned)

$ transvar canno -i 'MRE11A:c.592_593delGTinsTA' --ensembl --gseq

MRE11A:c.592_593delGTinsTA   ENST00000323929 (protein_coding)        MRE11A  -
   chr11:g.94209521_94209522delinsTA/c.592_593delinsTA/p.V198*       inside_[cds_in_exon_7]
   CSQN=Missense;codon_cDNA=592-593-594;aliases=ENSP00000325863;source=Ensembl       c
   hr11      94209520        TAC     TTA
MRE11A:c.592_593delGTinsTA   ENST00000323977 (protein_coding)        MRE11A  -
   chr11:g.94209521_94209522delinsTA/c.592_593delinsTA/p.V198*       inside_[cds_in_exon_7]
   CSQN=Missense;codon_cDNA=592-593-594;aliases=ENSP00000326094;source=Ensembl       c
   hr11      94209520        TAC     TTA
MRE11A:c.592_593delGTinsTA   ENST00000393241 (protein_coding)        MRE11A  -
   chr11:g.94209521_94209522delinsTA/c.592_593delinsTA/p.V198*       inside_[cds_in_exon_7]
   CSQN=Missense;codon_cDNA=592-593-594;aliases=ENSP00000376933;source=Ensembl       c
   hr11      94209520        TAC     TTA
MRE11A:c.592_593delGTinsTA   ENST00000540013 (protein_coding)        MRE11A  -
   chr11:g.94209521_94209522delinsTA/c.592_593delinsTA/p.V198*       inside_[cds_in_exon_7]
   CSQN=Missense;codon_cDNA=592-593-594;aliases=ENSP00000440986;source=Ensembl       c
   hr11      94209520        TAC     TTA

Another example of deletion

$ transvar ganno -i "chr2:g.234183368_234183379del" --ccds --gseq --seqmax 200

chr2:g.234183368_234183379del        CCDS2502.2 (protein_coding)     ATG16L1 +
   chr2:g.234183368_234183379delACTCATCCTGGT/c.841_852delACTCATCCTGGT/p.T281_G284delTHPG     inside_[cds_in_exon_8]
   CSQN=InFrameDeletion;left_align_gDNA=g.234183367_234183378delTACTCATCCTGG;una
   ligned_gDNA=g.234183368_234183379delACTCATCCTGGT;left_align_cDNA=c.840_851del
   TACTCATCCTGG;unalign_cDNA=c.841_852delACTCATCCTGGT;left_align_protein=p.T281_
   G284delTHPG;unalign_protein=p.T281_G284delTHPG;source=CCDS        chr2    234183366       ATA
   CTCATCCTGG        A
chr2:g.234183368_234183379del        CCDS2503.2 (protein_coding)     ATG16L1 +
   chr2:g.234183368_234183379delACTCATCCTGGT/c.898_909delACTCATCCTGGT/p.T300_G303delTHPG     inside_[cds_in_exon_9]
   CSQN=InFrameDeletion;left_align_gDNA=g.234183367_234183378delTACTCATCCTGG;una
   ligned_gDNA=g.234183368_234183379delACTCATCCTGGT;left_align_cDNA=c.897_908del
   TACTCATCCTGG;unalign_cDNA=c.898_909delACTCATCCTGGT;left_align_protein=p.T300_
   G303delTHPG;unalign_protein=p.T300_G303delTHPG;source=CCDS        chr2    234183366       ATA
   CTCATCCTGG        A
chr2:g.234183368_234183379del        CCDS54438.1 (protein_coding)    ATG16L1 +
   chr2:g.234183368_234183379delACTCATCCTGGT/c.409_420delACTCATCCTGGT/p.T137_G140delTHPG     inside_[cds_in_exon_5]
   CSQN=InFrameDeletion;left_align_gDNA=g.234183367_234183378delTACTCATCCTGG;una
   ligned_gDNA=g.234183368_234183379delACTCATCCTGGT;left_align_cDNA=c.408_419del
   TACTCATCCTGG;unalign_cDNA=c.409_420delACTCATCCTGGT;left_align_protein=p.T137_
   G140delTHPG;unalign_protein=p.T137_G140delTHPG;source=CCDS        chr2    234183366       ATA
   CTCATCCTGG        A