Lack of "GQ" value in output.vcf and some question about "Merging" step

[xxYaaoo]

Hello Dr.Chen,

1.I noticed that the example output.vcf file contained "GQ:GL:DPN:DPI" values, while my output.vcf for each sample only had a result of "GT". What might cause this problem? Any important step I had ignored?

2.When I checked my merge_output.vcf, I found that this vcf file did not contain all the insertions identified in each sample vcf file. I ran over the script of Combine_VCF_files.pl, it seemed like the close insertions would be combined in one region. However, some separate insertions were not in my merge_output.vcf, (for example: Sample1‘s output.vcf contained an insertion on Chr19, while there were no insertions located in Chr19 in merge_output.vcf) ... Why has it happened?

Sorry to bother, thank you so much!!

[xunchen85]

Hi,

could you provide more info how you get your output vcf? like what parameters you used to get it?

you are correct, insertions within a small window (e.g., 1500bp) will be merged. Regarding the insertions on chr19, I don't know what happened so far without more info. Is it a singleton? low quality? However, I think we did not filter low-quality loci in the combined script.

Best, Xun

[xxYaaoo]

Hello,

I have figured out the problem about "GQ" value in output.vcf. ~ But still are confused with merge step. Here are one output.vcf of my samples and my merge_output.vcf. I think the insertions with red marks also should be included in the merge.vcf, while they were not. And this missing situation happened in every input sample. what might lead to this problem~? (last one is my merge.vcf)

Thank you for your reply!

[xunchen85]

Hi,

Can you try to sort the individual VCF first before merging? Let me know if it doesn't work. You could also follow our protocol here: https://doi.org/10.1007/978-1-0716-2883-6_4.

Can you also check if you find these missing loci in the file containing consensus TE loci?

Xun

[xxYaaoo]

Hi, Dr.Chen

I followed the protocol and sorted individual VCF files before the merging step, but it didn't work. And the txt.consensus file did not contain those missing loci. What might cause this problem？~

Thank you！

[xunchen85]

Do you want to attach some example VCF files containing the problematic loci? I could help debug it?

If the consensus txt file does not have it, it should be something to do with either the VCF files or the Combine_VCF_files.pl script.

Best, Xun

[xxYaaoo]

Hi,

Here are my example merging.vcf file and two my sample vcf files (AM107 and AM102). My detecting step ran with the parameter "-t 24 -S 40 -r 150 -n 2 -G" and the following steps followed the protocol.

Thank you so much for your reply and help!

example.zip

[xunchen85]

Hi,

Thanks for sharing the example file and sorry for the wait due to the holiday break.

It was finally resolved and you could download the revised Combine_VCF_files.pl here and replace the original one: https://github.com/xunchen85/ERVcaller/blob/v1.4/Scripts/Combine_VCF_files.pl.

It was due to two bugs here relative to the row end problem and a small number of TE loci (e.g., one TE insertion on an entire chromosome).

ps, let me know if you have further questions!

Best, Xun

[xxYaaoo]

Hello Dr.Chen,

Thank you for your reply and help! I tried the new version of Combine_VCF_files.pl and the output merged VCF contained more insertions. But it seemed that the VCF still missed a few insertions. I uploaded some example files here (the merged VCF lacked the 'chr15 63082393' insertion in AM104 and 'chr5 168576151' insertion in AM101). What might cause this ？ maybe the special insertion position? .. example.zip

Thank you so much！

[xunchen85]

Hi,

Thanks for your feedback. It was corrected which was due to a similar bug. You can download the Combine_VCF_files.pl from the same link: https://github.com/xunchen85/ERVcaller/blob/v1.4/Scripts/Combine_VCF_files.pl.

After merging, you will now get 20 unique TE insertion loci. Let me know if you have further questions.

Thanks, Xun

[xxYaaoo]

Hello Dr.Chen,

I saw the latest update version of the Combine_VCF_files.pl. Thank you so much for your help! Really appreciate!

Best, Yaaoo