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Error running vcf2xg.sh on c. elegans #20
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Thank you for the feedback! |
I fixed the truncated reference problem. For the latter data, the gfa file seems to be generated at least. https://github.com/sjackman/gfalint can be used for validation of gfa file. |
Okay I've remove
and the stack-trace:
It's doesn't look like it generated the I have the following call sets if you are more familiar with one of them we can try that: |
We defined |
I've posted a follow up in the
Which format is this in? I tried Any idea why this odd output is being produced by |
Is it possible to try it again on the latest MoMI-G master? |
Okay making some progress now. I've tried again off of the latest MoMI-G master (
And test it's working:
Now I run
Should I be concerned about the |
Because the I need to create a What about the |
Actually there is a line in vcf that is not parsed by momig-tools, and I intend to output error message when it encounters such a line. But it won't work now due to a bug. I suppose the output pcf file might be insufficient. I'll fix it soon. |
After that, this configuration YAML file is needed to be loaded as the next step.
The fastest way is to copy this config file and change the file name of xg in the following config.yaml. |
Is it possible for you to try it on the latest master and tell me the output of MoMI-G script? I suppose the lines starting with |
Sure I can try that:
So this is the error output:
|
Okay so I now have a
However, I cannot find an example of GRCh
|
Thank you for reporting an error. I'll check it. |
I suspect this line is invalid. Usually, vcf file is described as a tab-delimited text as |
Luckily I have a number of variant call sets from a variety of tools so we can tell if this is unique to
For all of the VCF files I have I seem to get an error.
|
These errors might be caused due to different reasons. MoMI-G tools does not support Illumina SV callers explicitly. Is it possible to normalize each vcf file with https://github.com/fritzsedlazeck/SURVIVOR before running vcf2xg? (e.g. run |
I was just working with From
Merge:
Lot of errors from this:
Tried using |
SURVIVOR seems to add "chr" as a prefix of each reference genome to normalize, but the original reference genome is started with |
Please update SURVIVOR. I am not 100% sure which subcommand of SURIVOR is used, but I assume the merge . Thanks |
I also have similar error, like this:
And my vcf files were merged with |
Thank you for reporting. I assume some records in the vcf file are not supported in vcf2vg. I updated the way to report errors on |
First off, I have to say great job on the tool! I've played around with the practice data and now I'm very excited to try this tool out and show it to my laboratory. I've been evaluating ~10 tools for looking at SVs and yours by-far looks the most promising!
I'm getting an error trying to convert a
.VCF
to.xg
using thevcf2xg.sh
script on the reference genome (C. elegans) used for alignment.I tried another call set (
Delly
) to see if it's something specific to the format of VCF but got a similar error:The stack-trace from
Delly
is:Any idea what could be happening here? One thought is that chromosome in H. sapiens are usuallly labeled
chr1
but in C. elegans they are labeled (I
,II
,III
,IV
,V
,X
,MtDNA
) - not sure if this information helps?As for the
Reference :0-270000000
part I have no idea of the context of this number:270000000
? It seems like a very round number? The entire genome of C. elegans is ~100286401bp
.The text was updated successfully, but these errors were encountered: