Download the source code here: bcftools-1.25.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:

• New option --progress[=INT] in mpileup, norm and view to periodically print the current position (CHR:POS) to stderr, indicating how far a long-running command has progressed (#2559)

• Fix allele merging in norm and merge to preserve symbolic IDs and breakend contig names and respect their case during matching, as required by VCF specification.

• The -i/-e filtering expressions

  • Fix negated regular-expression (!~) filtering of string fields, which could incorrectly evaluate to true without testing the pattern (#2609)
    Changes affecting specific commands:

• bcftools call

  • To comply with the VCF specification, the INFO/MQ output tag is now declared as Type=Float rather than Type=Integer

• bcftools csq

  • New option --allow to selectively relax validation checks (#2584)

  • New option -F, --format to extend the consequence annotation with cds_position (position within the coding sequence and CDS length), exon (exon index and the number of exons), and exon_position (position within the exon and the exon length)

  • Fix a segfault caused by incorrect handling of symbolic ALT alleles. Support symbolic alleles at multiallelic sites.

• bcftools consensus

  • Fix -M masking of symbolic deletions and mixed multiallelic sites, including out-of-bounds accesses with overlapping variants and at FASTA region boundaries.

  • Fix REF span handling when applying sequence alleles at sites where INFO/END describes a longer symbolic allele.

• bcftools +fill-tags

  • Add two tags to annotate variant sequence context:
    INFO/CTX .. k-nt reference context centered at POS
    INFO/CpG .. CpG change relative to REF considering all ALTs;
    C=created, D=destroyed, B=both; N=CpG present and unchanged

  • Fix a bug where any sample of one or two characters is rejected (#1931, #1933)

• bcftools index

  • Make --nrecords with non-standard file extensions (#2588)

• bcftools +mendelian

  • Support sites with more than 64 alleles (#2603)

• bcftools mpileup

  • Fix INFO/MQBZ, BQBZ, RPBZ, SCBZ, MQSBZ and NMBZ at sites where more than 1290 reads share one quality or position bin, reachable at a single deep site or across the samples of a multi-sample call. The Mann-Whitney U tie correction was accumulated in 32-bit int and overflowed, which shrank the Z scores towards zero.

• bcftools norm

  • Left-align allele no matter which of INFO/SVLEN or INFO/END is present

  • Skip records whose alleles cannot safely be realigned together (#2605)

  • Realign long indels in linear time (#2604)

  • Recalculate INFO/AN,AC from genotype fields unless the new option --no-update is given (#2137, #548).

  • Extend the -c, --check-ref option for explicit control of output case, report the number of records changed (#2606)

  • Make -d exact consistent for sequence alleles differing only in case.

  • Fix incorrect allele mappings and associated annotations when atomizing (-a) multiallelic records after a compound variant (#2607)

• bcftools reheader

  • Better error reporting on invalid --samples file, don't segfault (#2538)

• bcftools sort

  • Add --threads and, in --verbose 4 mode or higher, print elapsed time

Download the source code here: bcftools-1.25.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.)