BCFtools 1.7 is now available from GitHub and SourceForge (Samtools and
HTSlib 1.7 were previously released on 26th January).



The main changes are listed below:

bcftools - changes v1.7

* `-i, -e` filtering: Major revamp, improved filtering by FORMAT fields
  and missing values. New GT=ref,alt,mis etc keywords, check the
  documentation for details.

* `query`: Only matching expression are printed when both the -f and -i/-e
  expressions contain genotype fields. Note that this changes the original
  behaviour. Previously all samples were output when one matching sample was
  found. This functionality can be achieved by pre-filtering with view and
  then streaming to query. Compare
        bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
        bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query 

* `annotate`: New -k, --keep-sites option

* `consensus`: Fix --iupac-codes output

* `csq`: Homs always considered phased and other fixes

* `norm`: Make `-c none` work and remove `query -c`

* `roh`: Fix errors in the RG output

* `stats`: Allow IUPAC ambiguity codes in the reference file; report the
  number of missing genotypes

* `+fill-tags`: Add ExcHet annotation

* `+setGt`: Fix bug in binom.test calculation, previously it worked only
  for nAlt<nRef!

* `+split`: New plugin to split a multi-sample file into single-sample
  files in one go

* Improve python3 compatibility in plotting scripts

Rob Davies              r...@sanger.ac.uk
The Sanger Institute    http://www.sanger.ac.uk/
Hinxton, Cambs.,        Tel. +44 (1223) 834244
CB10 1SA, U.K.          Fax. +44 (1223) 494919

The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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