vcf2kinship not finding samples in pedigree

[padlocke11180]

The latest update (20161018) available here, now sends an error when trying to generate kinship while including the ped file.

When running the following command:
../executable/vcf2kinship --inVcf example.vcf.gz --ped pheno --bn --xHemi --out example.output
Exclude [ 500 ] samples from VCF files because they do not exist in pedigree file or do not have sex
[ERROR] No samples left for analysis, aborting...

Earlier versions of the software did not have this problem.

[zhanxw]

Can you please tell me more about the problem:

Did you use the binary version or compile form the source-codes?
Which Linux distribution do you use?

Thanks.

[padlocke11180]

Hi Xiaowei, It's Adam formerly of Michigan. I downloaded the compiled binaries on Friday. My Linux version is: 3.0.0-16-server GNU/Linux, but it appears to be independent of linux as numerous collaborators have recently encountered the same problem. As I think I stated in the original post, this error seems to have cropped up in the most recent version of the software. Older versions all seemed to work fine. Please let me know if you need anything else. Adam

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On Mon, Feb 6, 2017 at 2:51 AM, zhanxw ***@***.***> wrote: Can you please tell me more about the problem: Did you use the binary version or compile form the source-codes? Which Linux distribution do you use? Thanks. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYXuDzqc5Sflw-jfgkC0qG7zifPIY7neks5rZt8rgaJpZM4L3QXq> .

[zhanxw]

Hi Adam,

Thanks very much for the information.
I have identified the bug, and will release a new version to fix it.

Best,
Xiaowei

[zhanxw]

This release provides the fix: https://github.com/zhanxw/rvtests/releases/tag/v2.0.1

Thanks!

[padlocke11180]

FYI, you did not update the version information/dates in the new version. may be confusing for some. Looks like the problem is fixed, though. Thanks!

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On Fri, Feb 10, 2017 at 2:15 AM, zhanxw ***@***.***> wrote: This release provides the fix: https://github.com/zhanxw/ rvtests/releases/tag/v2.0.1 Thanks! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYXuDy1Xapa-7aWORArVqtQJxHsUGRLSks5rbByigaJpZM4L3QXq> .

[zhanxw]

I have fixed the version information/dates in the new version. Thank you very much. Xiaowei On Fri, Feb 10, 2017 at 3:06 PM, padlocke11180 <notifications@github.com> wrote:

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FYI, you did not update the version information/dates in the new version. may be confusing for some. Looks like the problem is fixed, though. Thanks! On Fri, Feb 10, 2017 at 2:15 AM, zhanxw ***@***.***> wrote: > This release provides the fix: https://github.com/zhanxw/ > rvtests/releases/tag/v2.0.1 > > Thanks! > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#13 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AYXuDy1Xapa- 7aWORArVqtQJxHsUGRLSks5rbByigaJpZM4L3QXq> > . > — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAJoiGUuY6G43V2wb1_xXoXy1IHJ7ks9ks5rbNFigaJpZM4L3QXq> .