Search results

Issue in gff2gff.py script - does not generate the output file

Status: Open.

#2572 In samtools/bcftools;

· Maxime5G opened on Jun 25, 2026

Add optional progress output for long-running subcommands (mpileup, view, norm, index)

Status: Open.

#2559 In samtools/bcftools;

· carstenerickson opened on May 16, 2026

view -R: pathological performance with large single-base region sets (84M regions, 11+ hours unfinished)

Status: Open.

#2557 In samtools/bcftools;

· carstenerickson opened on May 16, 2026

Feature request : bcftools annotate and discordant chromosome notation

htslib-dependentCannot be fixed until htslib is fixedCannot be fixed until htslib is fixed

P2: Desirable

Status: Open.

#2549 In samtools/bcftools;

· lindenb opened on May 7, 2026

Feature request: use pedigree information for SNP calling

Status: Open.

#2546 In samtools/bcftools;

· mtiret opened on Apr 28, 2026

bcftools merge fills missing fields with "^@" instead of "."

needs-feedback

requires-test-case

Status: Open.

#2539 In samtools/bcftools;

· shmenolin opened on Apr 2, 2026

split-vep only prints first numerical value

requires-test-case

Status: Open.

#2516 In samtools/bcftools;

· sbaross opened on Mar 23, 2026

MIN_DP should be updated from DP not just other MIN_DP records. Production of a MIN_DP record when none are input.

requires-test-case

Status: Open.

#2515 In samtools/bcftools;

· bgulko opened on Mar 22, 2026

bcftools mpileup for a set of Illumina+HiFi reads

Status: Open.

#2511 In samtools/bcftools;

· sitaramrajaraman opened on Mar 12, 2026

feature request: polyploid variant calling

Status: Open.

#2508 In samtools/bcftools;

· taprs opened on Mar 2, 2026

bcftools annotate doesn't liftover fields from VCF with symbolic alleles if END in only one file.

requires-test-case

Status: Open.

#2507 In samtools/bcftools;

· ASLeonard opened on Mar 2, 2026

Incorrect allele ("2") in... when trying to merge, merged files

requires-test-case

Status: Open.

#2488 In samtools/bcftools;

· j-gillespie-dna opened on Dec 12, 2025