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Missing BAM index with <code>--region</code> 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

different gvcf output with same bed intervals

Status: Open.

#829 In freebayes/freebayes;

· ShannonDaddy opened on May 27, 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

[Question] Can you set the column header sample name? Or does it come from the BAM read group?

please file bugs only - use matrix insteadsee the READMEsee the README

Status: Open.

#819 In freebayes/freebayes;

· mheskett opened on Feb 6, 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

Two adjacent SNPs reported rather then a MNP?

bug

Status: Open.

#804 In freebayes/freebayes;

· Jesspalmer92 opened on Jun 17, 2024

Incongruencies in GT assignment

bug

Status: Open.

#793 In freebayes/freebayes;

· Virginia-b opened on Apr 4, 2024

Multiple bases returned instead of SNPs in one of the two replicates

bug

Status: Open.

#787 In freebayes/freebayes;

· NitKV opened on Mar 25, 2024