[Samtools-help] BCFtools 1.7

[Robert D. <rm...@sa...>]

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

https://sourceforge.net/projects/samtools/

https://github.com/samtools/bcftools/releases/tag/1.7

The main changes are listed below:

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bcftools - changes v1.7
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* `-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
   and
         bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

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


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