Hi,

I would like to use the "clump" function for my association analysis results which use 10000 Genomes imputed data (and I have many files), so I guess I need to use the 10000 Genomes genotypes as a reference file, but I am having trouble with this. I have downloaded the vcf files from the MACH website [here][1].

Then I thought I could use Plink 1.9 version that reads vcf and use directly the "clump" command here, but apparently there are issues with the vcf file for allele names (I would like to keep as many variants as possible), so I followed [this link][2] to convert from vcf to plink.

But I get a segfault error as soon as I type to this command:

    bcftools annotate -Ob -x ID chr21.test.vcf

which says:

```
[W::vcf_parse] INFO 'NS' is not defined in the header, assuming Type=String
Encountered error, cannot proceed. Please check the error output above.
```

I have tried to use `bcftools reheader -h` but it doesn't work, can someone please help?

Thank you!!

 [1]: http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G.2012-03-14.html
 [2]: http://apol1.blogspot.co.uk/2014/11/best-practice-for-converting-vcf-files.html
If you don't need to deal with split multi-allelic variants, Plink 1.9's `--set-missing-var-ids` flag should do a good enough job of assigning names. (You'll need a build from November 25th or later.)