Question

Right Align Variants

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6.2 years ago

avo ▴ 20

I am trying to right align variants. Most tools seem to left align by default. Is there a tool that right aligns variants?

variant annotation • 3.4k views

ADD COMMENT • link updated 18 months ago by DavidStreid ▴ 90 • written 6.2 years ago by avo ▴ 20

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Why do you want to right-align? The standard is to left-align.

When is a variant normalized?

A variant is normalized if and only if it is parsimonious and left aligned.

ADD REPLY • link 6.2 years ago by h.mon 35k

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I am trying to be consistent with HGVS guidelines and want to right align with respect to the gene. This issue seems to only come up for variants that on anti-sense genes.

ADD REPLY • link 6.2 years ago by avo ▴ 20

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this discussion can help a bit too : Indel Left/Right Alignment

I got a doubt now, in my mind aligner do alignment from the right and you need to correct it with GATK or samtools to realign in local for INDEL , am I right ?

ADD REPLY • link 6.2 years ago by Titus ▴ 910

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So, I also REALLY want to right align indels for the purposes of functional annotation. If I have a gene that is on the "minus" strand, the transcriptional machinery will read the (rightmost) sequence first so the protein (or truncated protein) will be only correctly identified if I have the right aligned variants. (we can have a long discussion about what do to for acceptor vs donor sites for splice sites.. but let's not..). Anybody know of a right shifting tool (p.s I know that CLC Bio and Atlas2 aligner align to the right, but I want a shifter.. not a complete realignment).

ADD REPLY • link 5.6 years ago by hugues.sicotte • 0

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In case others are interested -

ONLINE TOOL - mutalyzer
- e.g. NC_012920.1:m.513G>GCA -> NC_012920.1:m.523_524dup
LOCAL TOOL - biocommons/hgvs
- Setup seems very worth it for regular use as sequences not available in mutalyzer can be added to a local directory at defined by HGVS_SEQREPO_DIR environment variable

ADD REPLY • link 18 months ago by DavidStreid ▴ 90

score 0 · Answer 1 · 2018-09-04

Hello,

the hgvs recommendation to use the most 3' prime position cannot be fulfilled for g. and c. for genes that encode on the minus strand. The reference genome just now one direction.

In my opinion it is ok the left-align the variant when talking about the genome position, but using right-aligned position on transcript bases. snpEff is a tool that take this into account.

fin swimmer