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How to deal with swapped alleles

Status: Open.

#47 In freeseek/score;

· mirgin01 opened on Apr 16, 2026

Assertion failure / segfault in nw() during liftover of pangenome-derived VCF

Status: Open.

#46 In freeseek/score;

· teepean opened on Apr 6, 2026

liftover blocks when lifting joint VCFs from ROSMAP (bg37 -> hg19)

Status: Open.

#43 In freeseek/score;

· milcs40 opened on Jan 13, 2026

Munge plugin fails to read last column of TSV when comment character present

Status: Open.

#42 In freeseek/score;

· njd34 opened on Sep 19, 2025

Unable to install following instructions

Status: Open.

#37 In freeseek/score;

· PrestonMcDonald opened on Aug 4, 2025

Read LD from those 1kg_ldgm.*.bcf files

Status: Open.

#36 In freeseek/score;

· jielab opened on Aug 2, 2025

Handling of Phasing Information (PS Tags) with bcftools liftover

Status: Open.

#34 In freeseek/score;

· joaomsouto opened on Jul 2, 2025

Incorrect liftover - deletion within deleted region

Status: Open.

#32 In freeseek/score;

· lvclark opened on Jun 16, 2025

R wrapper of BCFTools score

Status: Open.

#31 In freeseek/score;

· sounkou-bioinfo opened on May 19, 2025

[W::bcf_hdr_check_sanity] GL should be declared as Number=G

Status: Open.

#30 In freeseek/score;

· John-Drake opened on May 12, 2025

Possible mismatch in header concerning target/query reference

Status: Open.

#29 In freeseek/score;

· emersonlds opened on Mar 27, 2025

liftover: invalid option -- 's'

Status: Open.

#28 In freeseek/score;

· liuhankui opened on Mar 20, 2025