Error in generating .HWE.vcf file about gbs_snp_filter HOT 4 CLOSED

Hi Omid,

There were a couple of things working against you here (not least some bugs in my code, but more on that in a moment!).

The first issue I needed to solve involved your GBS_SNP_filter.txt file:
-- populations.snp.vcf is the name you have in the GBS_SNP_filter.txt file, but this is not the correct name - your vcf file is actually called populations.snps.vcf
-- And as you figured out yourself already, “_.” was the separator for your ID column for the last run, but given the format has changed to having the locus separated from the SNP position by a colon, :. needs to be on line 8 of GBS_SNP_filter.txt, rather than _.*

The second issue involved your popmap.txt file: this didn’t have the same sample names as are in the vcf file. All of these sample names in the vcf file have “-sorted” on the end, and this is missing from your popmap.txt file. I tweaked this by:
mv popmap.txt oldpopmap.txt
sed -r 's/(.)(-[0-9][0-9][0-9])(.*)/\1\2-sorted\3/g' oldpopmap.txt > popmap.txt

After solving these issues, however, I then discovered a few bugs in the code left over from some of the bigger changes I made recently, so even if all your files had been correct the pipeline would probably have failed! (Sorry!) This should all be fixed now, and I’ve also placed the output files from running your files into the most recent dropbox folder you shared with me.

One thing I did notice is that it looks like the read depth for your SNPs is pretty low - is this something that you were expecting based on your sequencing run?

Thanks again for your patience!

Alana

P.S. I’ll leave this issue open for a week just in case you have any further issues and then close it if it is all good.

from gbs_snp_filter.

Hi dear Alana,
First of all I should make an excuse because of some mistakes in sending the files. Because I had many files and did that mistake to send the real file. But it should be mentioned that now the updated package works fluently on my vcf file, without any bug. Thanks for all your great supports.
Further to the read depth, yes you are right and I should check their quality and do some filtering based on the read depth, but generally speaking we didn't expect a high depth of coverage. Excuse me are there some thing you are thinking about? I mean do you have a suggestion to me?

Again I am really grateful for all your help.

Cheers,
Omid

from gbs_snp_filter.

Hi Omid,

No worries on the files - like I said, even if they had been correct, the code still had bugs in it! I was mostly asking about the read depth just because it appeared to be a fair bit lower than the previous run you had sent to me, and I just wanted to make sure that is what you'd expect (and not that the code was doing something additionally funny!), so no strong suggestions (other than if you are working with very low depth data but doing population genetics where you don't need to know individual genotypes, this kind of approach might be worth looking into: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12990).

Anyhow, as the pipeline is now working correctly for you, I'll go ahead and close this issue.

Good luck with your downstream analysis!

Alana

from gbs_snp_filter.

Hi Alana,
Well actually this vcf file was generated by someone else without considering some options, so maybe that is the most probable reason of the observed differences and I will regenerate it.
Thanks for sending the link of the paper and your support.

Cheers,
Omid

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