1.13

Download the source code here: bcftools-1.13.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.)

This release brings new options and significant changes in BAQ parametrization in bcftools mpileup. The previous behaviour can be triggered by providing the --config 1.12 option. Please see #1474 for details.

Changes affecting the whole of bcftools, or multiple commands:

• Improved build system

Changes affecting specific commands:

• bcftools annotate:

  • Fix rare a bug when INFO/END is present, all INFO fields are removed with bcftools annotate -x INFO and BCF output is produced. Then the removed INFO/END continues to inform the end coordinate and causes incorrect retrieval of records with the -r option (#1483)

  • Support for matching annotation line by ID, in addition to CHROM,POS,REF, and ALT (#1461)
    bcftools annotate -a annots.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END input.vcf

• bcftools csq:

  • When GFF and VCF/fasta use a different chromosome naming convention (e.g. chrX vs X), no consequences would be added. Newly the program attempts to detect these differences and remove/add the "chr" prefix to chromosome name to match the GFF and VCF/fasta (#1507)

  • Parametrize brief-predictions parameter to allow explicit number of amino acids to be printed. Note that the -b, --brief-predictions option is being replaced with -B, --trim-protein-seq INT

• bcftools +fill-tags:

  • Generalization and better support for custom functions that allow adding new INFO tags based on arbitrary -i, --include type of expressions. For example, to calculate a missing INFO/DP annotation from FORMAT/AD, it is possible to use:
    -t 'DP:1=int(sum(FORMAT/AD))'
    Here the optional ":1" part specifies that a single value will be added (by default Number=. is used) and the optional int(...) adds an integer value (by default Type=Float is used).

  • When FORMAT/GT is not present, the INFO/AF tag will be newly calculated from INFO/AC and INFO/AN.

• bcftools gtcheck:

  • Switch between FORMAT/GT or FORMAT/PL when one is (implicitly) requested but only the other is available

  • Improve diagnostics, printing warnings when a line cannot be matched and the number of lines skipped for various reasons (#1444)

  • Minor bug fix, with PLs being the default, the --distinctive-sites option started to require explicit --error-probability 0

• bcftools index:

  • The program now accepts both data file name and the index file name. This adds to user convenience when running index statistics (-n, -s)

• bcftools isec:

  • Always generate sites.txt with isec -p (#1462)

• bcftools +mendelian:

  • Consider only complete trios, do not crash on sample name typos (#1520)

• bcftools mpileup:

  • New --seed option for reproducibility of subsampling code in HTSlib

  • The SCR annotation which shows the number of soft-clipped reads now correctly pools reads together regardless of the variant type. Previously only reads with indels were included at indel sites.

  • Major revamp of BAQ. Please see #1474 for details. The previous behaviour can be triggered by providing the --config 1.12 option.

  • Thanks to improvements in HTSlib, the removal of overlapping reads (which can be disabled with the -x, --ignore-overlaps options) is not systematically biased any more (samtools/htslib#1273)

  • Modified scale of Mann-Whitney U tests. Newly INFO/*Z annotations will be printed, for example MQBZ replaces MQB.

• bcftools norm:

  • Fix Type=Flag output in norm --atomize (#1472)

  • Atomization must not discard ALT=. records

  • Atomization of AD and QS tags now correctly updates occurrences of duplicate alleles within different haplotypes

  • Fix a bug in atomization of Number=A,R tags

• bcftools reheader:

  • Add -T, --temp-prefix option

• bcftools +setGT:

  • A wider range of genotypes can be set by the plugin by allowing specifying custom genotypes. For example, to force a heterozygous genotype it is now possible to use expressions like: c:'m|M' c:0/1 c:0

• bcftools +split-vep:

  • New -u, --allow-undef-tags option

  • Better handling of ambiguous keys such as INFO/AF and CSQ/AD. The -p, --annot-prefix option is now applied before doing anything else which allows its use with -f, --format and -c, --columns options.

  • Some consequence field names may not constitute a valid tag name, such as "pos(1-based)". Newly field names are trimmed to exclude brackets.

• bcftools +tag2tag:

  • New --QR-QA-to-QS option to convert annotations generated by Freebayes to QS used by BCFtools

• bcftools +trio-dnm:

  • Add support for sites with more than four alleles. Note that only the four most frequent alleles are considered, the model remains unchanged. Previously such sites were skipped.

  • New --use-NAIVE option for a naive DNM calling based solely on FORMAT/GT and expected Mendelian inheritance. This option is suitable for pre-filtering.

  • Fix behaviour to match the documentation, the --dnm-tag DNG option now correctly outputs log scaled values by default, not phred scaled.

  • Fix bug in VAF calculation, homozygous de novo variants were incorrectly reported as having VAF=50%

  • Fix arithmetic underflow which could lead to imprecise scores and improve sensitivity in high coverage regions

  • Allow combining --pn and --pns to set the noise thresholds independently