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Sentieon
sentieon-cli
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Merge Dev changes
- #42
#42
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DonFreed
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Oct 31, 2026
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Merge Dev changes
#42
DonFreed
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Commits on Oct 7, 2026
Add the `--pop_vcf` argument to the DNAscope pipeline
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Add `UltimaReadFilter` to DNAscope calling with an Ultima bundle
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Commits on Oct 8, 2026
Update the pangenome CNV scripts to combine_sv_cnv 2.0.1
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Commits on Oct 9, 2026
Update the pangenome CNV scripts to combine_sv_cnv 2.1.0
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Relax `dnascope.model` under `--skip_small_variants`; add hybrid SE preset
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Cap KMC at 128 threads
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Commits on Oct 13, 2026
Pass `--dbsnp` to GVCFtyper
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Write a gVCF with `dnascope-hybrid --gvcf`
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Keep the hybrid second calling pass inside `--bed`
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Update the CNV scripts to combine_sv_cnv 2.1.2; assume sex chromosome ploidies when the sex is unknown
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Commits on Oct 15, 2026
Keep the input QUAL and drop FILTER in the `--pop_vcf` transfer
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Read the Ultima platform from `shortReadPlatform` in `dnascope`
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Fill the gVCF positions spanned only by a dropped variant record
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Select the hybrid realignment regions from a VCF-mode pass 1
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Stream the gVCF-mode hybrid scripts through `vcfconvert`
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Increment version
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Commits on Oct 26, 2026
Keep only the shard contig in the `--pop_vcf` transfer merge inputs
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Update Dockerfile base image
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Use the published image name in the README; update the base image label
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Write rejected CNV segments and take the combine preset from the bundle
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Commits on Oct 27, 2026
Update KMC to the v3.2.4-pipe3 build
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Split pangenome alignment into one lane per NUMA node
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Hand indel2cnv's variants to workers one at a time
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Run vg haplotypes alongside bwa when both fit in memory
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Commits on Oct 28, 2026
Name each alignment lane's job, and use one -K for every pangenome run
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Merge pull request #41 from haodongchen/claude/pangenome-large-hosts-dev
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