bcftools consensus

• Fix a bug which prevented reading fasta files containing empty lines in their entirety (#2424)

• Fix a bug which causes --absent miss some absent positions

bcftools csq

• Add support for complex substitutions, such as AC>TAA

bcftools +fill-tags

• Fix header formatting error for INFO/F_MISSING which must be Number=1 (#2442)

• Make -t 'F_MISSING' work with -S groups.txt (#2447)

bcftools gtcheck

• The program is now able to process gVCF blocks. Newly, monoallelic sites are excluded only when the site is monoallelic in both query and genotype file. The new option --keep-refs allows to always include monoallelic sites.

• Fix an error in parsing -i/-e command line options where the qry: and gt: prefix was not stripped (#2432)

bcftools mpileup

• Make -d, --max-depth 0 set the depth to unlimited (#2435)

bcftools norm

• Make the -i/-e filtering option work for all options, such as line merging and duplication removal (#2415)

bcftools query

• Numerical functions, such as SUM(INFO/DP), would previously return the value 0 when executed on missing values. This was incorrect, newly a missing value is printed.

bcftools reheader

• Add options --samples-list and --samples-file to allow renaming samples from a list of samples on command line, rather than from a file of sample names (#2383)

bcftools +split-vep

• Fix the option -A, --all-fields, it was not working properly and could lead to a segfault (#2473)