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:steven.da...@fda.hhs.gov]
> Sent: Thursday, November 17, 2016 3:24 PM
> To: samtools-help@lists.sourceforge.net
> 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
>
>
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