bcftools release 1.15.1:
* bcftools annotate
- New `-H, --header-line` convenience option to pass a header
line on command line, this complements the existing `-h,
--header-lines` option which requires a file with header lines
* bcftools csq
- A list of consequence types supported by `bcftools csq` has
been added to the manual page. (#1671)
* bcftools +fill-tags
- Extend generalized functions so that FORMAT tags can be filled
as well, for example:
bcftools +fill-tags in.bcf -o out.bcf -- \
-t 'FORMAT/DP:1=int(smpl_sum(FORMAT/AD))'
- Allow multiple custom functions in a single run. Previously the
program would silently go with the last one, assigning the same
values to all (#1684)
* bcftools norm
- Fix an assertion failure triggered when a faulty VCF file with
a '-' character in the REF allele was used with `bcftools norm
--atomize`. This option now checks that the REF allele only
includes the allowed characters A, C, G, T and N. (#1668)
- Fix the loss of phasing in half-missing genotypes in variant
atomization (#1689)
* bcftools roh
- Fix a bug that could result in an endless loop or incorrect
AF estimate when missing genotypes are present and the
`--estimate-AF -` option was used (#1687)
* bcftools +split-vep
- VEP fields with characters disallowed in VCF tag names by the
specification (such as '-' in 'M-CAP') couldn't be queried.
This has been fixed, the program now sanitizes the field names,
replacing invalid characters with underscore (#1686)