Incorrect translation when the HGVS string does not contain a reference or alt allele

[melissacline]

I've come across this problem with strings such as NM_007294.3:c.1209dup - which IMHO should actually be NM_007294.3:c.1209dupT (which is how ClinVar represents the variant), but mutalyzer claims that NM_007294.3:c.1209dup is valid HGVS... When I parse its name with

chrom, offset, ref, alt = hgvs.parse_hgvs_name(variant, genome, get_transcript=get_transcript)

I get the results that ref and alt are both 'C', where alt should be 'CC'. If there's a way around this, please let me know!

Thanks!

[mbosio85]

Hi,
I had the same issue and edited the init.py file in a couple of points
A disclaimer: It works for me because I have a small set to convert, I use genomic coordinates and no transcript in my conversion. If you apply these changes double check that it works fine before implementing in production
1- insert a clause in get_vcf_alleles() [the if=='dup' part)

def get_vcf_allele(hgvs, genome, transcript=None):
    """Get an VCF-style allele from a HGVSName, a genome, and a transcript."""
    chrom, start, end = hgvs.get_vcf_coords(transcript)
    _, alt = hgvs.get_ref_alt(
        transcript.tx_position.is_forward_strand if transcript else True)
    ref = get_genomic_sequence(genome, chrom, start, end)
    if hgvs.mutation_type == 'dup' and alt=='':
       alt = 2*ref[1:]
    if hgvs.mutation_type in _indel_mutation_types:
        # Left-pad alternate allele.
        alt = ref[0] + alt
    return chrom, start, end, ref, alt`

2- Commented out some lines in get_ref_alt()

  def get_ref_alt(self, is_forward_strand=True):
        """Return reference and alternate alleles."""
        if self.kind == 'p':
            raise NotImplementedError(
                'get_ref_alt is not implemented for protein HGVS names')
        alleles = [self.ref_allele, self.alt_allele]

        # Represent duplications are inserts.
        #if self.mutation_type == "dup":
        #    alleles[0] = ""
        #    alleles[1] = alleles[1][:len(alleles[1]) / 2]

        if is_forward_strand:
            return alleles
        else:
            return tuple(map(revcomp, alleles))

If you plan to do the same remember to reinstall the package once modified.
hope it helps,
Mattia