gVCF output option not working

Question

gVCF output option not working

biorococo opened this issue a year ago · comments

Clair-trio won't output gVCF format when enabling "--gvcf"

There is no printed error other than:

cat: 'test/tmp/gvcf_tmp_output/*.tmp.g.vcf': No such file or directory
FileNotFoundError: [Errno 2] No such file or directory: 'SortVcf'

Let me know if there is any other info you need. Thanks.

Junhao · Answer 1 · Fri Mar 31 2023 19:39:38 GMT+0800 (China Standard Time)

Thanks for your message.

Currently, Clair3-Trio doesn't provide the function to output the gVCF file. The "--gvcf" option on the help page is a legacy option and is not currently functional. Sorry for any confusion regarding the gVCF output option in Clair3-Trio.

And we updated the repo and docker image version without the "--gvcf" option on the help page.

Ruibang Luo · Answer 2 · Wed Apr 05 2023 17:28:13 GMT+0800 (China Standard Time)

@biorococo it takes some engineering efforts to add support for GVCF in Clair3-Trio, but it's doable. Could you share with us how would you like to use Clair3-Trio so we can better plan for the upgrade.

Ruibang Luo · Answer 3 · Tue Apr 11 2023 12:56:32 GMT+0800 (China Standard Time)

GVCF output added to v0.5

biorococo · Answer 4 · Tue Apr 11 2023 17:32:14 GMT+0800 (China Standard Time)

Thanks a lot for reopening the issue and add this output so quickly! will be helpful for downstream analysis. I will give this new version a try.

biorococo · Answer 5 · Thu Apr 13 2023 18:53:44 GMT+0800 (China Standard Time)

Hi again, I got my gVCF using the new version! although I'm getting the following error when using bcftools on the gvcf produced:

[W::vcf_parse_info] INFO 'T' is not defined in the header, assuming Type=String

For reference see INFO fields in header:
##INFO=<ID=P,Number=0,Type=Flag,Description="Result from pileup calling">
##INFO=<ID=F,Number=0,Type=Flag,Description="Result from full-alignment calling">

Also see some example records:
chr1 10108 . C CT,<NON_REF> 14.40 PASS T GT:GQ:DP:AF 0/1:14,0:27:0.5556,990,990,990
chr1 10199 . A C,<NON_REF> 8.24 PASS T GT:GQ:DP:AF 0/1:8,0:27:0.2593,990,990,990

Junhao · Answer 6 · Fri Apr 14 2023 11:55:19 GMT+0800 (China Standard Time)

Hi,

Thanks for your information, the error is caused by a missing header line in the gvcf output.

Adding a line in the gvcf output like:

##INFO=<ID=T,Number=0,Type=Flag,Description="Result from trio calling">

will fix this error.

I will fix it in one week and let you know when the mistake is fixed.

Junhao · Answer 7 · Tue Apr 25 2023 19:00:48 GMT+0800 (China Standard Time)

Hi, the gVCF header problem is fixed at v0.6. thanks.