ddrichel

Mutect2: drop in SNV specificity/precision between v.4.1.8.1 and 4.1.9.0

44

We noticed a strong drop in precision for SNVs (~10% for tumor-normal mode, ~20% in tumor-only mode) between releases 4.1.7.0 and 4.2.6.0. With more testing using the HCC1395 somatic benchmark...

INV, DEL, DUP with huge SVLENs in sniffles 2.0.7

7

Re-opening the previously reported issue https://github.com/fritzsedlazeck/Sniffles/issues/235, as it persists in sniffles 2.0.7 and we are still looking for a reasonable solution to filter FP calls without losing too many TPs....

bedtools intersect (v.2.30.0) seems to not handle 0-length intervals correctly. Example for length 1 and 2: $ cat a.bed 1 1 10000 cat b1.bed 1 5 6 $ bedtools2/bin/bedtools intersect...