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 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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