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

[Robert D. <rm...@sa...>]

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

If not, you can't find anything else, and you only want to do a few of 
them, it might be possible to break out pysam and write something.  If you 
want to do lots, then a C program would probably be the way forward - it 
doesn't look like it would be too difficult.

Rob Davies              rm...@sa...
The Sanger Institute    http://www.sanger.ac.uk/
Hinxton, Cambs.,        Tel. +44 (1223) 834244
CB10 1SA, U.K.          Fax. +44 (1223) 494919


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