bcftools release 1.18:

Download the source code here: bcftools-1.18.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

Changes affecting the whole of bcftools, or multiple commands:

• Support auto indexing during writing BCF and VCF.gz via new --write-index option

Changes affecting specific commands:

• bcftools annotate

  • The -m, --mark-sites option can be now used to mark all sites without the need to provide the -a file (#1861)

  • Fix a bug where the -m function did not respect the --min-overlap option (#1869)

  • Fix a bug when update of INFO/END results in assertion error (#1957)

• bcftools concat

  • New option --drop-genotypes

• bcftools consensus

  • Support higher-ploidy genotypes with -H, --haplotype (#1892)

  • Allow --mark-ins and --mark-snv with a character, similarly to --mark-del

• bcftools convert

  • Support for conversion from tab-delimited files (CHROM,POS,REF,ALT) to sites-only VCFs

• bcftools csq

  • New --unify-chr-names option to automatically unify different chromosome naming conventions in the input GFF, fasta and VCF files (e.g. "chrX" vs "X")

  • More versatility in parsing various flavors of GFF

  • A new --dump-gff option to help with debugging and investigating the internals of hGFF parsing

  • When printing consequences in nonsense mediated decay transcripts, include 'NMD_transcript' in the consequence part of the annotation. This is to make filtering easier and analogous to VEP annotations. For example the consequence annotation 3_prime_utr|PCGF3|ENST00000430644|NMD is newly printed as 3_prime_utr&NMD_transcript|PCGF3|ENST00000430644|NMD

• bcftools gtcheck

  • Add stats for the number of sites matched in the GT-vs-GT, GT-vs-PL, etc modes. This information is important for interpretation of the discordance score, as only the GT-vs-GT matching can be interpreted as the number of mismatching genotypes.

• bcftools +mendelian2

  • Fix in command line argument parsing, the -p and -P options were not functioning (#1906)

• bcftools merge

  • New -M, --missing-rules option to control the behavior of merging of vector tags to prevent mixtures of known and missing values in tags when desired

  • Use values pertaining to the unknown allele (<*> or <NON_REF>) when available to prevent mixtures of known and missing values (#1888)

  • Revamped line matching code to fix problems in gVCF merging where split gVCF blocks would not update genotypes (#1891, #1164).

• bcftool mpileup

  • Fix a bug in --indels-v2.0 which caused an endless loop when CIGAR operator H or P was encountered

• bcftools norm

  • The -m, --multiallelics + mode now preserves phasing (#1893)

  • Symbolic <DEL.*> alleles are now normalized too (#1919)

  • New -g, --gff-annot option to right-align indels in forward transcripts to follow HGVS 3'rule (#1929)

• bcftools query

  • Force newline character in formatting expression when not given explicitly

  • Fix -H header output in formatting expressions containing newlines

• bcftools reheader

  • Make -f, --fai aware of long contigs not representable by 32-bit integer (#1959)

• bcftools +split-vep

  • Prevent a segfault when -i/-e use a VEP subfield not included in -f or -c (#1877)

  • New -X, --keep-sites option complementing the existing -x, --drop-sites options

  • Force newline character in formatting expression when not given explicitly

  • Fix a subtle ambiguity: identical rows must be returned when -s is applied regardless of -f containing the -a VEP tag itself or not.

• bcftools stats

  • Collect new VAF (variant allele frequency) statistics from FORMAT/AD field

  • When counting transitions/transversions, consider also alternate het genotypes

• plot-vcfstats

  • Add three new VAF plots