df <- importFromTable() troubles about qtlseqr

[bmansfeld]

Hey Juan,
Sorry you met a bug.
It would be helpful if you shared just the top 100 rows of your CSV that way I could figure out how to trouble shoot.
It seems that something must be funky with the column identification and renaming.
You can email me the file to bmansfeld --at-- danforthcenter.org
Have you tried parsing your VCF using GATK VariantsToTable and using importFromGATK()?
Hope to be able to help,
Ben

[juanlu16]

Hi Ben It's ok, don't worry, and thank you very much for replying and for the help. Sorry for not emailing you at danforthcenter.org. When I try I get an error. On the other hand, I have not been able to find your contact on that same page either. I created the table with libreoffice calc. I saved it with the parameters I indicated in the bug I wrote in github. This is how the table looks like when I open it again with libreoffice calc:  I don't know if it can be seen clearly, if not, let me know and I will send you a larger image. However, there is one thing that makes me doubt if the table is well generated. When I open it with excel, the aspect that presents:  I do not know if the problem is in the generation of the table, or if the program does not detect the columns. In the screenshots you can only see 30-40 lines, the screen does not catch more. On the other hand, if you wish, I can take images of more lines, in case you want to review the file more. On the other hand, answering the question about whether I have tried with the data coming from GATK and with the function "importFromGATK()". In this case I have not tried it since I do not have gatk correctly installed and it does not generate the vcf files correctly. It is because of this problem, that I used bcftools mpileup and bcftools call for I get vcf files. Again, thank you very much for your help Ben, it will be very useful, I am very grateful. Best regards, Juan Luis El jue, 31 mar 2022 a las 3:38, Ben Mansfeld ***@***.***>) escribió:

…

Hey Juan, Sorry you met a bug. It would be helpful if you shared just the top 100 rows of your CSV that way I could figure out how to trouble shoot. It seems that something must be funky with the column identification and renaming. You can email me the file to bmansfeld --at-- danforthcenter.org Have you tried parsing your VCF using GATK VariantsToTable and using importFromGATK()? Hope to be able to help, Ben — Reply to this email directly, view it on GitHub <#51 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWEOHRBITGWNPQDGBX5A333VCT62BANCNFSM5R57AUYQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bmansfeld]

QTLseqr::importFromTable() uses the default sep = "," to separate the columns looks like you have a tab or space separating the columns when you save the file so when excel is looking for , in the csv it does not find it and neither does QTLseqr.
Try making sure you are either exporting a csv or a tsv and importing the relevant file using the correct sep argument in QTLseqr::importFromTable()

hope that helps.
Ben