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bcftools reheader discards the VCF header if there's no variants (ie creates a 0B file) #356

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drmjc opened this issue Nov 26, 2015 · 1 comment
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bcftools reheader discards the VCF header if there's no variants (ie creates a 0B file) #356

drmjc opened this issue Nov 26, 2015 · 1 comment
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1.3.1

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@drmjc
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drmjc commented Nov 26, 2015

Hi,
I was using bcftools reheader v1.2 to rename samples & all was fine. But in VCF files where there are no variants (as can happen in our automated somatic pipeline), instead of getting a vcf.gz file with the header and updated sample names, I got an empty file.

The specific message was:

FIXME: No body in the file: strelka.passed.somatic.snvs.vcf.gz

Could you please just print the header after updating the sample ID's instead?
cheers.
@mcshane mcshane added the bug label Jan 20, 2016
pd3 added a commit to pd3/bcftools that referenced this issue Jan 22, 2016
@pd3
Reheader allow empty body with vcf.gz. Fixes samtools#356
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pd3 commented Jan 22, 2016

Hi, this is now fixed. Thanks for reporting the bug

@jmarshall jmarshall added this to the 1.3.1 milestone Apr 20, 2016
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