Hello!
After updating Delly from v1.5.0 to v1.7.2, significant differences were observed in the VCF files generated for the same sample.
The command used for both versions:
delly call -x human.hg38.excl.tsv -g GRCh38.d1.vd1.fa sample.bam
Overall, there are approximately 2826 lines changed out of about 37,000 total records
- For example, some variants present in
v1.5.0 (e.g. INV00002476, INV00002129, INV00002219, DUP00015556) disappeared, while new variants appeared in v1.7.2 (e.g. BND00037261, BND00039914, DEL00030967).
Differences Delly v1.5.0 (left) vs v1.7.2 (right):
- All chromosomes: Values in fields
GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV changed
Could you please clarify the reasons for these differences? Are they expected changes due to updates in the algorithm or parameters?
Also, we noticed that Delly runs about 3,5 times faster now - thank you for the improvement!
Hello!
After updating Delly from
v1.5.0tov1.7.2, significant differences were observed in the VCF files generated for the same sample.The command used for both versions:
Overall, there are approximately 2826 lines changed out of about 37,000 total records
v1.5.0(e.g. INV00002476, INV00002129, INV00002219, DUP00015556) disappeared, while new variants appeared inv1.7.2(e.g. BND00037261, BND00039914, DEL00030967).Differences
Dellyv1.5.0(left) vsv1.7.2(right):chr2: SNV IDs changedGT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RVchangedCould you please clarify the reasons for these differences? Are they expected changes due to updates in the algorithm or parameters?
Also, we noticed that
Dellyruns about 3,5 times faster now - thank you for the improvement!