1.24

Download the source code here: bcftools-1.24.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.)

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Changes affecting the whole of bcftools, or multiple commands:

• Calculation of MAC and MAF in -i/-e filtering expressions

  • Minor allele count and minor allele frequency were calculated incorrectly at multiallelic sites.

Changes affecting specific commands:

• bcftools +af-dist

  • New -s, --samples to print per-sample HWE probability, geometric mean

• bcftools annotate

  • Fix a bug in annotation renaming via --rename-annots and -c NEW:=OLD, where renaming INFO/TAG would simultaneously rename also FORMAT/TAG (#2489)

  • Allow annotation of Number=A,R INFO tags from tab-delimited files when alleles are split across multiple records.

• bcftools cnv

  • Fix off-by-one error in reporting HMM qualities

• bcftools convert

  • Make --gvcf2vcf work around malformed gVCF records where INFO/END overlaps the next record

• bcftools csq

  • Fix a start_lost issue in haplotype mode: suppress formatting of amino-acid changes of variants that follow on the same haplotype, but still print DNA changes (#2543)

  • Add a new -G, --greedy option which forces the program to check intronic consequences after feature hits (#2548)

• bcftools +fill-tags

  • Fix custom functions to use rounding instead of truncation when converting to integer, so that -t 'MAC:1=float(MAF*AN)' and -t 'MAC:1=int(MAF*AN)' return consistent values.

  • Support per-population annotation for embedded functions, such as in -t 'MAC:1=int(MAF*AN)' -S groups.txt (#2514)

• bcftools +mendelian2

  • Number of fixes and improvements, including a fix in assigning 1X vs 2X inheritance rules with -p (#2545)

• bcftools merge

  • Fixes in memory access with localized alleles, it could result in printing printing trailing garbage in localized FORMAT fields (#2520)

  • Add new -m exact mode to merge only records with the exact same alleles (#2498)

• bcftools mpileup

  • Remove unused experimental INFO/MIN_PL_SUM annotation

  • Add new FORMAT/QM annotation, to be used with the new bcftools +trio-dnm3 --use-ALM model.

• bcftools norm

  • Fix a bug in splitting Type=String FORMAT fields via -a and -m (#2476)

  • Fix erroneous INFO/END recalculation of symbolic alleles (#2500).

  • Added --no-realign[=NUM] to skip realignment during normalization; when NUM is given, only events longer than NUM bp are skipped. This deprecates the option --do-not-normalize (equivalent to --no-realign=0). See also #2500.

  • Convert ambiguous IUPAC bases to their lexicographically first concrete base, as required by the VCF specification (#2551)

• bcftools +prune

  • When pruning by window length in base pairs, one out-of-window record would be incorrectly accessed. Not only this by-one error would calculate LD in unwanted pair of records, it also led to unexpected behavior when the first out-of-window record would change by filtering (#2475)

• bcftools roh

  • Fix off-by-one error in reporting HMM qualities

• bcftools +split-vep

  • Add support for SnpEff output, add a new option --csq-field, --consequence-field which allows to override the default consequence field name 'Consequence' (#2566)

  • Stop converting consequence severity to lower case

• bcftools stats

  • Fix per-sample stats when samples provided in different order via -s/-S (#2534)

• bcftools +tag2tag

  • Make the advertised default for -t, --threshold match the implementation: 0, not 0.1. Also clarify that the value is the maximum allowed GP error (call if GP >= 1 - FLOAT), not a minimum GP threshold (#2564)

• bcftools +trio-dnm3

  • Add a new TrioDNM model and make it the new default. To prevent confusion, the old +trio-dnm2 plugin was removed and replaced with +trio-dnm3. The original +trio-dnm3 model can be run as
    bcftools +trio-dnm3 --use-ALM

• bcftools view

  • Fix the -v/V, --types/--exclude-types option to work with ref and extend for all types supported by htslib: snps,indels,mnps,ref,bnd,other,overlap (#2567)

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Download the source code here: bcftools-1.24.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.)