Table 2. Site-specific and sample-specific filters used by the different groups to detect de novo mutations (DNMs) in Heineken (difference in the other steps of the pipeline in Table 2—source data 1).
Table 2—source data 1. Details on the methodology and filtering criteria applied by the five different pipelines to estimate the mutation rate on the common pedigree.
elife-73577-table2-data1.xlsx (12.2KB, xlsx)
| Research group | Candidate DNMs | Site-specific filters | Sample-specific filters | Additional filters |
|---|---|---|---|---|
| CV | 18 | GATK Best Practices hard filter criteria |
0.5 × dpind < DP < 2 × dpind GQ > 40 AD > 0 0.25 < AB < 0.75 |
|
| RW | 22 | QD < 2.0 MQ < 40.0 FS > 60.0 SOR > 3.0 MQRankSum < –12.5 ReadPosRankSum < –8.0 |
20 < DP < 80 GQ > 20 AD > 0 0.35 < AB |
Alternative allele on both strands |
| TT | 27 | Remove variants in recent repeats or in homopolymers of AAAAAAAAAA or TTTTTTTTTT | DP > 10 GQ > 20 AD > 0 0.25 < AB |
Overlap three different variant callers Filter on LCR |
| LB | 28 | QD < 2.0 FS > 20.0 MQ < 40.0 MQRankSum < –2.0 MQRankSum > 4.0 ReadPosRankSum < –3.0 ReadPosRankSum > 3.0 SOR > 3.0 |
0.5 × dpind < DP < 2 × dpind GQ > 60 AD none 0.3 < AB < 0.7 |
Manual curation (six candidates removed) |
| SB | 32 | FS > 30.0 MQRankSum < –10 MQRankSum > 10 ReadPosRankSum < –2.5 ReadPosRankSum > 2.5 BaseQRankSum < –13 BaseQRankSum > 13 |
10 < DP < 2× dpind GQ > 55 AD > 0 0.3 < AB |
Alternative allele in both strands. lowQ AD2 > 1 |
LB: Lucie Bergeron; SB: Søren Besenbacher; CV: Cyril Versoza; TT: Tychele Turner; RW: Richard Wang.