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SNP and INS cannot be retrieved simultaneously

Status: Open.

#850 In freebayes/freebayes;

· xue-QJ opened on Jul 28, 2026

--strict-vcf outputs large GQ values in float scientific notation

Status: Open.

#849 In freebayes/freebayes;

· xonq opened on Jul 23, 2026

Would FreeBayes Be recommended if we aligned our sequences using pangenome reference

Status: Open.

#848 In freebayes/freebayes;

· eabebe-tech opened on Jun 2, 2026

Typo in parameter doc

Status: Open.

#847 In freebayes/freebayes;

· SamGG opened on May 29, 2026

Carry over IUPAC codes instead of replacing them with N

Status: Open.

#846 In freebayes/freebayes;

· cmfield opened on Apr 22, 2026

Freebayes crashes with segmentation fault when the number of contigs in the reference is large (300000)

bug

Status: Open.

#841 In freebayes/freebayes;

· puthick opened on Feb 3, 2026

The rule GenerateFreebayesRegions in the snakemake-freebayes-parallel.smk doesn't work

bug

Status: Open.

#839 In freebayes/freebayes;

· SLAment opened on Dec 5, 2025

Missing BAM index with --region should exit 1

bug

Status: Open.

#831 In freebayes/freebayes;

· schorlton-bugseq opened on Jul 19, 2025

vcfuniq insufficient to remove duplicates when merging vcfs

bug

Status: Open.

#830 In freebayes/freebayes;

· nikostr opened on Jun 25, 2025

Understanding INFO fields output from freebayes

help wanted

Status: Open.

#821 In freebayes/freebayes;

· Sgornard opened on Feb 18, 2025

Sample order output in joint VCF can change unexpectedly

bug

Status: Open.

#820 In freebayes/freebayes;

· mheskett opened on Feb 10, 2025

A "strict" VCF with with FORMAT/GQ set to INT is produced without using the --strict-vcf option

help wanted

Status: Open.

#818 In freebayes/freebayes;

· mheskett opened on Feb 6, 2025