Download the source code here: bcftools-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

Changes affecting the whole of bcftools, or multiple commands:

• The -i/-e filtering expressions and -f formatting in query

  • Add a new function smpl_COUNT()/sCOUNT() which returns the number of elements (#2423)

Changes affecting specific commands:

• bcftools annotate

  • Make dynamic variables read from a tab-delimited annotation file (#2151) work also for regions. For example, while the first command below was functional, the second was not (#2441)
    bcftools annotate -a ann.tsv.gz -c CHROM,POS,-,SCORE,~STR -i'TAG={STR}' -k in.vcf
bcftools annotate -a ann.tsv.gz -c CHROM,BEG,END,SCORE,~STR -i'TAG={STR}' -k in.vcf

• 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)

Download the source code here: bcftools-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)