Try DeepVariant as replacement for freebayes

[marc-sturm]

• try DeepVariant
  • benchmark performance with NA12878x2_93
  • benchmark runtime (1, 5, 10 threads, maybe on GPU)
    • test deepvariant-gpu
    • benchmark runtime and performance for gpu version
  • check if gVCF can be created and used to perform multi-sample analysis
    • gVCF can be created
    • check if it can be used to perform multi-sample analysis

[KilianIlius]

Runtime:

10 threads:
Job 879294 (php) Complete
User = ahiliuk1
Queue = [email protected]
Host = SRV012.img.med.uni-tuebingen.de
Start Time = 01/08/2025 17:15:01
End Time = 01/09/2025 00:47:49
User Time = 00:06:23
System Time = 00:03:07
Wallclock Time = 07:32:48
CPU = 117:05:28
Max vmem = 33.956G
Exit Status = 0

5 threads:
Job 879295 (php) Complete
User = ahiliuk1
Queue = [email protected]
Host = SRV010.img.med.uni-tuebingen.de
Start Time = 01/08/2025 17:15:31
End Time = 01/09/2025 15:05:33
User Time = 00:03:49
System Time = 00:01:41
Wallclock Time = 21:50:02
CPU = 577:59:23
Max vmem = 14.197G
Exit Status = 0

1 thread:
Job 879296 (php) Complete
User = ahiliuk1
Queue = [email protected]
Host = SRV015.img.med.uni-tuebingen.de
Start Time = 01/08/2025 17:15:46
End Time = 01/11/2025 07:01:35
User Time = 97:30:49
System Time = 13:23:35
Wallclock Time = 61:45:49
CPU = 110:54:24
Max vmem = 18.904G
Exit Status = 0

Former performance:
#name options date average_depth expected_snvs expected_indels snv_sensitivity snv_ppv snv_f1 snv_genotyping_accuracy indel_sensitivity indel_ppv indel_f1 indel_genotyping_accuracy all_sensitivity all_ppv all_f1 all_genotyping_accuracy
NA12878x2_93_var 2025-01-10 18:13:04 40.98 3256373 495309 0.9934 0.9944 0.9939 0.9993 0.9754 0.9938 0.9845 0.9847 0.9911 0.9927 0.9943 0.9974

Performance with DeepVariant:
#name options date average_depth expected_snvs expected_indels snv_sensitivity snv_ppv snv_f1 snv_genotyping_accuracy indel_sensitivity indel_ppv indel_f1 indel_genotyping_accuracy all_sensitivity all_ppv all_f1 all_genotyping_accuracy
vc_deep_NA12878x2_93_t10 2025-01-09 00:47:46 40.98 3256373 495309 0.9941 0.9993 0.9967 0.9997 0.9910 0.9970 0.9940 0.9986 0.9937 0.9963 0.9990 0.9996