1.11

Download the source code here: bcftools-1.11.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:

• Filtering -i/-e expressions

  • Breaking change in -i/-e expressions on the FILTER column. Originally it was possible to query only a subset of filters, but not an exact match. The new behaviour is:

    Expression	Result
    FILTER="A"	Exact match, for example "A;B" does not pass
    FILTER!="A"	Exact match, for example "A;B" does pass
    FILTER~"A"	Both "A" and "A;B" pass
    FILTER!~"A"	Neither "A" nor "A;B" pass

  • Fix in commutative comparison operators, in some cases reversing sides would produce incorrect results (#1224; #1266)

  • Better support for filtering on sample subsests

  • Add SMPL_*/S* family of functions that evaluate within rather than across all samples. (#1180)

• Improvements in the build system

Changes affecting specific commands:

• bcftools annotate:

  • Previously it was not possible to use --columns =TAG with INFO tags and the --merge-logic feature was restricted to tab files with BEG,END columns, now extended to work also with REF,ALT.

  • Make annotate -TAG/+TAG work also with FORMAT fields. (#1259)

  • ID and FILTER can be transferred to INFO and ID can be populated from INFO. However, the FILTER column still cannot be populated from an INFO tag because all possible FILTER values must be known at the time of writing the header (#947; #1187)

• bcftools consensus:

  • Fix in handling symbolic deletions and overlapping variants. (#1149; #1155; #1295)

  • Fix --iupac-codes crash on REF-only positions with ALT=".". (#1273)

  • Fix --chain crash. (#1245)

  • Preserve the case of the genome reference. (#1150)

  • Add new -a, --absent option which allows to set positions with no supporting evidence to "N" (or any other character). (#848; #940)

• bcftools convert:

  • The option --vcf-ids now works also with -haplegendsample2vcf. (#1217)

  • New option --keep-duplicates

• bcftools csq:

  • Add misc/gff2gff.py script for conversion between various flavors of GFF files. The initial commit supports only one type and was contributed by @flashton2003. (#530)

  • Add missing consequence types. (PR #1203; #1292)

  • Allow overlapping CDS to support ribosomal slippage. (#1208)

• bcftools +fill-tags:

  • Added new annotations: INFO/END, TYPE, F_MISSING.

• bcftools filter:

  • Make --SnpGap optionally filter also SNPs close to other variant types. (#1126)

• bcftools gtcheck:

  • Complete revamp of the command. The new version is faster and allows N:M sample comparisons, not just 1:N or NxN comparisons. Some functionality was lost (plotting and clustering) but may be added back on popular demand.

• bcftools +mendelian:

  • Revamp of user options, output VCFs with mendelian errors annotation, read PED files (thanks to Giulio Genovese).

• bcftools merge:

  • Update headers when appropriate with the '--info-rules *:join' INFO rule. (#1282)

  • Local alleles merging that produce LAA and LPL when requested, a draft implementation of samtools/hts-specs#434 (#1138)

  • New --no-index which allows to merge unindexed files. Requires the input files to have chromosomes in th same order and consistent with the order of sequences in the header. (PR #1253; samtools/htslib#1089)

  • Fixes in gVCF merging. (#1127; #1164)

• bcftools norm:

  • Fixes in --check-ref s reference setting features with non-ACGT bases. (#473; #1300)

  • New --keep-sum switch to keep vector sum constant when splitting multiallelics. (#360)

• bcftools +prune:

  • Extend to allow annotating with various LD metrics: r^2, Lewontin's D' (PMID:19433632), or Ragsdale's D (PMID:31697386).

• bcftools query:

  • New %N_PASS() formatting expression to output the number of samples that pass the filtering expression.

• bcftools reheader:

  • Improved error reporting to prevent user mistakes. (#1288)

• bcftools roh:

  • Several fixes and improvements
    • the --AF-file description incorrectly suggested "REF\tALT" instead of the correct "REF,ALT". (#1142)
    • RG lines could have negative length. (#1144)
    • new --include-noalt option to allow also ALT=. records. (#1137)

• bcftools scatter:

  • New plugin intended as a convenient inverse to concat (thanks to Giulio Genovese, PR #1249)

• bcftools +split:

  • New --groups-file option for more flexibility of defining desired output. (#1240)

  • New --hts-opts option to reduce required memory by reusing one output header and allow overriding the default hFile's block size with --hts-opts block_size=XXX. On some file systems (lustre) the default size can be 4M which becomes a problem when splitting files with 10+ samples.

  • Add support for multisample output and sample renaming

• bcftools +split-vep:

  • Add default types (Integer, Float, String) for VEP subfields and make --columns - extract all subfields into INFO tags in one go.