update to 1.22 · Pull Request !11 · src-openEuler/bcftools

1. update to 1.22

Changes affecting the whole of bcftools, or multiple commands:

Add support for matching lines by ID via the --pair-logic and --collapse options (#1739)
 The -i/-e filtering expressions
   The expressions now properly match the regex negation of missing values, e.g. -i 'TAG!~"\."' (#2355)
   Added support for Fisher's exact test
 Add the option -v, --verbosity INT to all bcftools commands and plugins. Verbosity values bigger than 3 are passed to the underlying HTSlib library so that the user can investigate network issues and other problems occurring at the library level.

Changes affecting specific commands:

bcftools annotate
  Fix Number in the header definition of transferred FILTER and ID tags (#2335)
bcftools call
  The -s, --samples option was not working properly, now also supporting sample negation as advertised in the manual page, e.g. -s ^sample1,sample2 to include all samples but sample1 and sample2 (#2380)

bcftools consensus
  Preserve entire missing gVCF blocks with --missing (#2350)
  Fixed a bug, the -S, --samples-file option is no longer ignored (#2398)

bcftools convert
  The command convert --gvcf2vcf was not filling the REF allele when BCF was output (#243)

bcftools csq
  Check the input GFF for features outside transcript boundaries and extend the transcript to contain the feature fully (#2323)
  Add experimental support for alternative genetic code tables, accessible via a new option -C, --genetic-code (#2368)
  Change in the --unify-chr-names option, no automatic sequence name modification is attempted anymore, the prefixes to trim must be given explictly. For example, if run with --unify-chr-names chr,Chromosome,-, the program will trim the "chr" prefix in the VCF, "Chromosome" in the GFF, leaving the fasta unchanged (#2378)

bcftools +fill-tags
  Thanks to the extension of filtering expressions with Fisher's exact test, the plugin can now be used to add FT annotation (#1582)

bcftools merge
  Preserve phasing in half-missing genotypes (#2331)
  The option --merge none is expected to create no new multiallelic sites, but it should allow to merge, say, A>C with A>C,AT (#2333)
  Make --merge both work with indel-only records; for example, the multiallelic site G>GT,T should be merged with G>GT (#2339)
  Do not merge symbolic alleles unless they have not just the same type, eg. <DEL>, but also length, i.e the INFO/END coordinate (#2362)
  Fix a bug where an incorrectly formatted gVCF file with overlapping blocks would trigger an infinite loop in the program (#2410)

bcftools mpileup
  The -r/-R option newly merge overlapping regions, preventing the output of duplicate sites

bcftools norm
  Print the number of removed duplicate sites in the final statistics (#2346)
  Preserve the original alleles in --old-rec-tag when --check-ref s requested (#2357)
  Print a warning when INFO/SVLEN is not defined as Number=A (#2371)

plot-vcfstats
  Make the option -s, --sample-names functional again (#2353)

bcftools +prune
  New option to remove or annotate clusters of sites within a window

bcftools query
  The functions used in -i/-e filtering expressions (such as SUM, MEDIAN, etc) can be now used in formatting expressions (#2271). If the VCF contains INFO/AD and FORMAT/AD, try:
    bcftools query test.vcf -f '%CHROM:%POS \t [ %AD] \t [ %sSUM(FMT/AD)]'
    bcftools query test.vcf -f '%CHROM:%POS \t [ %AD] \t [ %SUM(FMT/AD)]'
    bcftools query test.vcf -f '%CHROM:%POS \t [ %AD] \t   %SUM(FMT/AD)'
    bcftools query test.vcf -f '%CHROM:%POS \t [ %AD] \t   %SUM(INFO/AD)'
  Make it possible to refer to the ID column from the FORMAT expression (#2337)
    bcftools query test.vcf -f 'ID=%ID  ID=[ %/ID]  vs  FMT_ID=[ %ID]'

bcftools roh
  New visualization tool misc/roh-viz, see below

bcftools +setGT
  Support for setting missing genotypes with arbitrary ploidy via -n c:./. (#2303)

bcftools +split-vep
  The -s, --select option was extended to print only one consequence. Previously it was possible to select a single transcript (e.g., the one with the worst consequence), and it was possible to filter by consequence severity (e.g., missing or worse), but in some cases multiple consequences are reported within a single transcript (e.g., start_lost&splice_region). The extended option allows to print the worst part, for example as --select primary:missense+:worst

bcftools +trio-dnm2
  Fix a problem with --strictly-novel option which would neglect the presence of the apparent de novo allele in the father for male offspring
  Fix a problem with uncalled mosaic chrX variants in males

roh-viz
  HTML/JavaScript visualization of bcftools/roh output and homozygosity rate.
bcftools +vrfs
  New experimental plugin for scoring variants and assess site noisiness (variant read frequency profiles) from a large number of unaffected parental samples

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