Closed razshaikh closed 2 years ago
Thanks @razshaikh for letting me know about this error! Could you share your VCF with me, so I can test and make sure that it can be fixed? It might be related to the underlying library (cyvcf), but I will check and see if I can fix it.
best, Sigve
Hi @sigven, thank you for your response, Really appreciated. Please find the sample VCF below: test_sample_run.zip
Hi @sigven, any suggestions on how to solve this issue.
Thanks and Regards, Razin
Hi @razshaikh, I am working on it, sorry for the delayed response.
Hi @sigven, I understand you must be having other tasks on your hand. I really appreciated you looking into it. Thank you. Best Wishes, Razin
Hi again @razshaikh,
Been digging a bit, and it seems this matter is related to how cyvcf2 works. See this related issue, for instance.
Either way, I have now added a simple check for this in vcf2tsv (v0.3.6), which should fix the error you encountered. On another note, your test VCF was full of other strange formatting errors, so I had to change it quite a bit for a test run.
kind regards, Sigve
Hi @sigven, Hope you are doing well.
Thank you for the update. I checked it, and it works for the 'GQ' values, but other values still has the same issue.
For example: the values in AD column, if any value is missing and has a period('.') instead, the latest script still replaces it with '-2147483648'.
Let me know if you have any suggestions for it.
Thanks and regards, Razin
Hi @sigven
I have added a pull request, let me know if that makes sense.
Best wishes, Razin
Input VCF File values
Output TSV File values