HKU-BAL/Clair

GVCF output

GuillaumeHolley opened this issue · 6 comments

GuillaumeHolley commented

Hello,

Would be possible to add a GVCF output to Clair? GLnexus could be used on the output GVCFs to make a joint VCF afterwards.

Thank you for your help.

Best regards,
Guillaume

aquaskyline commented

GVCF output added in Clair2.

GuillaumeHolley commented

Great, thanks :) Will try it asap.

aquaskyline commented

Clair2 will be available as soon as early 2021. Thank you for your suggestion!

GuillaumeHolley commented

Oh my bad, I thought that Clair was the v2 of ClairVoyante. Thank you for your work!

YanfengJi commented

Hello,
I am trying to process PacBioCLR data with this version of Clair and hope to get GVCF. As mentioned above, GVCF output was added in Clair2, but I did not find the corresponding parameter in the help document. May I ask what parameters should I use.
Thanks

aquaskyline commented

Clair doesn't support GVCF output, please use https://github.com/HKU-BAL/Clair3