f0e64850da
-- Reduce the min read length to 10 bp in the filterNonPassingReads in the HC. Now that we filter out reads before genotyping, we have to be more tolerant of shorter, but informative, reads, in order to avoid a few FNs in shallow read data -- Reduce the min usable base qual to 8 by default in the HC. In regions with low coverage we sometimes throw out our only informative kmers because we required a contiguous run of bases with >= 16 QUAL. This is a bit too aggressive of a requirement, so I lowered it to 8. -- Together with the previous commit this results in a significant improvement in the sensitivity and specificity of the caller NA12878 MEM chr20:10-11 Name VariantType TRUE_POSITIVE FALSE_POSITIVE FALSE_NEGATIVE TRUE_NEGATIVE CALLED_NOT_IN_DB_AT_ALL branch SNPS 1216 0 2 194 0 branch INDELS 312 2 13 71 7 master SNPS 1214 0 4 194 1 master INDELS 309 2 16 71 10 -- Update MD5s in the integration tests to reflect these two new changes |
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| .. | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| compression/reducereads | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| haplotypecaller | ||
| indels | ||
| phasing | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||