Trim variant

[martijnvermaat]

I don't mean this to be pulled in as-is, but rather to start discussion.

Standard convention with VCF is to place an indel at the left-most position, but some tools add additional context to the right of the sequences (e.g. samtools). These common suffixes are undesirable when comparing variants, for example in variant databases.

The trim_common_suffix function removes these common suffixes, forcing the INDEL to the left.

For example, to get trimmed reference and alternate alleles for a VCF record:

>>> print record
Record(CHROM=chr1, POS=152195728, REF=ATTTTTTTTTTT, ALT=['ATTTTTTTTTT', 'ATTTTTTTTT'])
>>> trim_common_suffix(record.REF, *record.ALT)
['ATT', 'AT', 'A']

Or if you only want to work with the first alternate allele:

>>> trim_common_suffix(record.REF, record.ALT[0])
['AT', 'A']

If such functionality should ever be included in PyVCF, a few ideas:

• Per allele is difficult, since alleles in a record all share the same reference. It could be a .trimmed() method on Call objects, returning a pair of trimmed reference and trimmed variant.
• Per record could be done with a flag in the Reader constructor, which would cause all records to be trimmed. Or provide separate fields next to the existing REF and ALT fields, containing the trimmed versions.

But I think trimming per allele is in practice most useful.

Related to this would be to really left-align the INDEL as far as possible, making use of a reference file, and thereby possibly modifying the start position of the variant. The GATK LeftAlignVariants module and the Freebayes --left-align-indels do this.

Other opinions?

[brentp]

in the above, where you have the example of "only work[ing] with the first alternate allele. Is that

>>> trim_common_suffix(record.REF, record.ALT[0])

 instead of `*record.ALT`?

looks useful to me.

[martijnvermaat]

Fixed, thanks for catching that.

[jamescasbon]

Anyone have an opinion on this? Is it ready for merge?

Looks like an upstream problem, but accept it is useful.