It’s a very important step to combine multiple samples’ gvcf files together in the pipeline of joint calling.
In GATK, it could be done with CombineGVCFs.
But in Parabricks 4.0, I can’t find the corresponding software.
And in previous version, some join calling functions has been implemented, such as CombineGVCFs (but can only input 2 or 3 gvcfs) and GLNexus.
So is there any future plan to add the function back and free the limitation of the number of gvcf files?
I am also having issues with the genotypegvcf command. It seems to only be taking one g.vcf file in the input. If I specify a directory with multiple g.vcf files it throws this error →
[PB Info 2023-Jan-04 08:22:55] ------------------------------------------------------------------------------
[PB Info 2023-Jan-04 08:22:55] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Jan-04 08:22:55] || Version 4.0.0-1 ||
[PB Info 2023-Jan-04 08:22:55] || genotypegvcf ||
[PB Info 2023-Jan-04 08:22:55] ------------------------------------------------------------------------------
[PB Warning 2023-Jan-04 08:22:55][src/PBLocalFile.cpp:48] Failed to open file /home/user/project/gvcf_test/0.g.vcf
[PB e[31mErrore[0m 2023-Jan-04 08:22:55][-unknown-:0] Received signal: 11
Exiting…
Could not run genotypegvcf
Exiting pbrun …
Interestingly 0.g.vcf is not one of my gvcf files … Im not sure where that is coming from. THis is the code Im running