Re: [Samtools-help] bcftools isec retain duplicates [EXT]

[James B. <jk...@sa...>]

On Thu, Aug 04, 2022 at 08:43:58AM +0100, Thomas Juettemann wrote:
> Hi Rob,
> Thanks for looking into it. Unfortunately isec keeps only the first record.

If you're not after a full intersection of only-in-A only-in-B and
in-both, then it's possible you could use filtering options instead.

Eg "bcftools view -T A.vcf.gz B.vcf.gz" will report records from B that
overlap locations listed in A.  It doesn't need to a be BED file as
it'll auto-detect the file format.

> > On Tue, 2 Aug 2022, Thomas Juettemann wrote:
> >
> > > I came across a "transcript-based" VCF file, meaning a variant can be
> > > present multiple times but belonging to a different transcript. See
> > > "FIle 1" below as an example. I am finding myself in the unfortunate
> > > situation of having to intersect ("File 2")  and retain all records
> > > with the same position and REF/ALT ("Desired output").
> > > Long shot: Is that possible?
> >
> > Does "bcftools isec" (https://www.htslib.org/doc/bcftools.html#isec) do
> > what you want?  The "Extract and write records from A shared by both A and
> > B using exact allele match" example in the manual page sounds like it
> > might:
> >
> >     bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz

I think this means that in the above example, multiple transcripts in
B that overlap the coordinates in A will still be shown.  If you need
the reverse, then it'd need another command with A and B swapped
around.

I'm not sure this is exactly the same thing, but it's worth an
experiment with a few simple examples to validate it.  (Take care with
complex variants and not just SNPs to check "overlap" works as you
expect when indels are present.)

James

-- 
James Bonfield (jk...@sa...)
The Sanger Institute, Hinxton, Cambs, CB10 1SA


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