hi,all
When I use bcftools merge to merge vcf, the indels will be automatically
Left-aligned. Could this be optional?
Thanks!--
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Problem solved with "--merge all" command line option.
-Original Message-
From: Thomas W. Blackwell [mailto:tbla...@umich.edu]
Sent: Monday, November 21, 2016 9:45 AM
To: Davis, Steven
Cc: samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] bcftools merge : multipl
ave 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
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
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 QUALFILTER INFO
b
Dear Sir/Madam,
I have two VCF file and I would like to two them using the following command:
bcftools merge -m none -i 'AC:sum,AN:sum' -O z -o merge.vcf.gz file1.vcf.gz
file2.vcf.gz
But I couldn't figure out now the get the summary INFO field to work?
For example:
File1.vcf:
chr1914876
Hi Sébastien,
sorry that the error message is not clear enough. The parser (htslib)
gives the warning
[W::vcf_parse] FILTER 'NOCALL' is not defined in the header
which sometimes can be ignored, sometimes not.
For merging, missing definitions are critical and `bcftools merge`
should exit with a
Like I said, I ran the command without output options to have merged.vcf
on stdout.
And this way I could see the broken row.
Sébastien
Le 03-07-2015 15:36, Thomas W. Blackwell a écrit :
> I would put the command line flags before the input file names:
>
>bcftools merge -O z -o merged.vcf.gz
I would put the command line flags before the input file names:
bcftools merge -O z -o merged.vcf.gz 002.vcf.gz 003.vcf.gz
- tom blackwell -
On Fri, 3 Jul 2015, S�bastien Letort wrote:
Hi,
I've got 2 small vcf files that I want to merge.
Hi,
I've got 2 small vcf files that I want to merge.
bcftools merge 002.vcf.gz 003.vcf.gz -O z -o merged.vcf.gz
The output is empty
I had this warning, but I don't think it is linked to the problem
[W::vcf_parse] FILTER 'NOCALL' is not defined in the header
The filter not defined: NOCALL
I trie
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