Repository Issue Activity (beta)

#1098 --num_shards and --postprocess_cpus do not limit CPU usage during the later stages of DeepVariant

#1099 trim_reads_for_pileup is unintentionally enabled when alt_aligned_pileup="none"

#486 Support for Multi-nucleotide Variant (MNV) Calling

#1100 Support Ultima sequencing data

#1095 Interpretation of GQ, PL and GT for sites with low-confidence calls

#1097 Proposal: evaluate the longest-ALT pileup as the sole model input

#1096 Variant not called in v1.9.0 that was called by v1.6.1

#1093 DeepSomatic 1.10.0 make_examples_somatic is OOM-killed on a 25 kb ONT tumor-only region due to unbounded read materialization

#1091 RNA editing sites in MASSEQ model

#1094 Fatal error from invalid switch line in PACBIO phased calls

#280 Strange false positive call

#1060 Segmentation fault in make_examples when running DeepVariant 1.10.0 with PacBio HiFi BAM

#1092 Pangenome aware deepvariant for long read data

#1079 Error when running phasing with WGS sample.

#1081 DeepVariant on BGI / DNBSEQ PE150 data — model suitability and QC guidance

#1090 Apple Silicon native port: Homebrew formula available for packaging

#1003 Empty queue in call variants output processing hangs job

#1080 Imputed data in vcf

#1077 Error running conda build

#1074 Training datasets for MASSEQ model

#1078 call_variants_outputs did not pass sanity check

#1072 Training deepvariant on RNA TUMOR ONLY SOMATIC variant calling

#1076 GPU warnings when running CPU steps.

#1051 issue resuming unfinished model training cont'd

#1071 singularity v.10 ValueError: NOT_FOUND: Failed to load FASTA file [] and/or index file [] Please double check these files exist and are of the correct format.