Error in generating the .ld.vcf file (the final step) about gbs_snp_filter HOT 4 CLOSED

Hi Omid - thanks for sending me these files and logging this error. I'm away at a conference for the next two days, but will get to it after I get back. Sorry my pipeline keeps throwing bugs at you!

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Hi Omid - thanks for sending me these files and logging this error. I'm away at a conference for the next two days, but will get to it after I get back. Sorry my pipeline keeps throwing bugs at you!

It is highly appreciated. I really like your pipeline since it is very user friendly.

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HI Omid - sorry for the delay, but this bug should now be fixed! It was a bit of superfluous code present from way back in the beginning when I was writing/testing out the LD filter. It would only affect any vcf file that had less than five populations but more than two loci in LD, so took it took your dataset to reveal it. Sorry again for the inconvenience - I've run the code through and the 'final' vcf file is present in the Dropbox folder you shared with me, but if you want to run it again yourself, if you clone the current version of the directory that should work too!

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HI Omid - sorry for the delay, but this bug should now be fixed! It was a bit of superfluous code present from way back in the beginning when I was writing/testing out the LD filter. It would only affect any vcf file that had less than five populations but more than two loci in LD, so took it took your dataset to reveal it. Sorry again for the inconvenience - I've run the code through and the 'final' vcf file is present in the Dropbox folder you shared with me, but if you want to run it again yourself, if you clone the current version of the directory that should work too!

Hi dear Alana,

Thank you very much for all your great helps. Now it is working properly and I got the vcf out puts.

Yours sincerely,

Omid

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