Re: [Samtools-help] bcftools merge : multiple rows per position

[Davis, S. <Ste...@fd...>]

Problem solved with "--merge all" command line option.

-----Original Message-----
From: Thomas W. Blackwell [mailto:tb...@um...] 
Sent: Monday, November 21, 2016 9:45 AM
To: Davis, Steven
Cc: sam...@li...
Subject: Re: [Samtools-help] bcftools merge : multiple rows per position

Steve  -

Totally guessing.  Is there something different between the two 
.vcf input files being merged which bcftools would interpret as 
an informative ALT allele in the file with 4 samples and a "." 
ALT allele in the file with 20 samples ?  Something different in 
the .vcf header blocks ?  Something different in the formatting ? 
Or, literal "." alternate alleles ?

Is it plink or plink-seq which allows you to reset the alternate 
allele for each marker ?  (Might be easier than hand-editing the 
.vcf file if that is what's needed.)

Overall, I suspect that there's something about the input .vcf 
files which is causing this, and later versions of bcftools are 
stricter about checking it than version 1.1.  Again, just guessing.

 	 	 	 	 	 	-  tom blackwell  -

On Mon, 21 Nov 2016, Davis, Steven wrote:

> Anyone have any ideas?  Still looking for help with this.
>
> From: Davis, Steven [mailto:Ste...@fd...]
> Sent: Thursday, November 17, 2016 3:24 PM
> To: sam...@li...
> Subject: [Samtools-help] bcftools merge multiple rows per position
>
> Hello support,
>
> I am merging VCF files with bcftools merge using this command:
>
> bcftools merge --info-rules NS:sum -o outFilePath dir/*.gz
>
> Previously, using bcftools 1.1, the output VCF file contained one row per position, like this:
>
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
> barref  1094    .       A       G       .       PASS    NS=24
> barref  1221    .       G       A       .       PASS    NS=24
> barref  2015    .       G       A       .       PASS    NS=24
>
> Using newer version of bcftools 1.2 or 1.3.1, I am seeing two rows per position, like this:
>
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
> barref  1094    .       A       .       .       PASS    NS=20
> barref  1094    .       A       G       .       PASS    NS=4
> barref  1221    .       G       .       .       PASS    NS=20
> barref  1221    .       G       A       .       PASS    NS=4
> barref  2015    .       G       .       .       PASS    NS=20
> barref  2015    .       G       A       .       PASS    NS=4
>
> How can I get one row of output per position when using bcftools 1.2 or higher?
>
> Thanks,
>
> Steve Davis
> Office of Analytics and Outreach
> FDA Center for Food Safety and Applied Nutrition
> 5100 Paint Branch Pkwy
> College Park, MD 20740
> Office: 240-402-4834
>
>