samtools/bcftools 1.9

on GitHub

The bcftools-1.9.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.

• annotate

  • REF and ALT columns can be now transferred from the annotation file.

  • fixed bug when setting vector_end values.

• consensus

  • new -M option to control output at missing genotypes

  • variants immediately following insersions should not be skipped. Note however, that the current fix requires normalized VCF and may still falsely skip variants adjacent to multiallelic indels.

  • bug fixed in -H selection handling

• convert

  • the --tsv2vcf option now makes the missing genotypes diploid, "./." instead of "."

  • the behavior of -i/-e with --gvcf2vcf changed. Previously only sites with FILTER set to "PASS" or "." were expanded and the -i/-e options dropped sites completely. The new behavior is to let the -i/-e options control which records will be expanded. In order to drop records completely, one can stream through "bcftools view" first.

• csq

  • since the real consequence of start/splice events are not known, the aminoacid positions at subsequent variants should stay unchanged

  • add --force option to skip malformatted transcripts in GFFs with out-of-phase CDS exons.

• +dosage: output all alleles and all their dosages at multiallelic sites

• +fixref: fix serious bug in -m top conversion

• -i/-e filtering expressions:

  • add two-tailed binomial test

  • add functions N_PASS() and F_PASS()

  • add support for lists of samples in filtering expressions, with many samples it was impractical to list them all on the command line. Samples can be now in a file as, e.g., GT[@samples.txt]="het"

  • allow multiple perl functions in the expressions and some bug fixes

  • fix a parsing problem, @ was not removed from @filename expressions

• mpileup: fixed bug where, if samples were renamed using the -G (--read-groups) option, some samples could be omitted from the output file.

• norm: update INFO/END when normalizing indels

• +split: new -S option to subset samples and to use custom file names instead of the defaults

• +smpl-stats: new plugin

• +trio-stats: new plugin

• Fixed build problems with non-functional configure script produced on some platforms