[Vcftools-help] deletion-insertion event representation

[Jonathan H. <jw...@sa...>]

Hi All,

First I will apologise if this has already been brought up on the list - I had a quick look through the archives and couldnt see any related topics. 

I am currently attempting to convert some of our pindel variant call data into VCF. Pindel generates a number of different call types including 'Deletions', 'Insertions' and 'Complex'. In this case complex calls manifest themselves as a deletion AND insertion at the same location - or another way to look at it, a region of reference sequence that is replaced by a novel chunk of sequence.

While deletions and insertions are well covered in the VCF documentation I am unsure how to proceed in the case of such complex events.

My initial idea was to set include the deleted region under ref and include the inserted sequence under alt:

#CHROM	POS	ID	REF	ALT	QUAL	......
6	1396302	.	TCACGCTG	TAACAC	.	.	......

My alternative would be to represent the event in two components and link them together using the id field :

#CHROM	POS	ID	REF	ALT	QUAL	......
6	1396302	1	TCACGCTG	T	.	.	......
6	1396302	1	T	TAACAC	.	.	......

The third would be to use the Structural Variation notation to represent a breakpoint with inserted sequence and eroded bases but this seems very heavy weight.

I would prefer the former over the latter two as there is less repetition and I believe is more human readable. However, I as I am unsure what is the accepted convention I thought I would throw it out into the open and see how other people are representing variants like this.

Many thanks in advance,
Jon



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