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Carry over IUPAC codes instead of replacing them with N

Status: Open.

#846 In freebayes/freebayes;

· cmfield opened on Apr 22, 2026

freebayes-parallel Error - Pipe -k

Status: Open.

#843 In freebayes/freebayes;

· desmodus1984 opened on Mar 9, 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

Heterozygous calls (0/1) generated despite violating --min-alternate-fraction and --min-alternate-count thresholds

Status: Open.

#840 In freebayes/freebayes;

· wxijia03 opened on Feb 1, 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

Issue with --min-coverage Option in FreeBayes

bug

Status: Open.

#817 In freebayes/freebayes;

· chantisakee opened on Dec 17, 2024

SNP but not seen in IGV

bug

Status: Open.

#815 In freebayes/freebayes;

· cpwater opened on Oct 16, 2024