Beta release 0.1.13 (1 March, 2011)
The most important though largely invisible modification is the change of the
order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
generated by samtools older than r921 inclusive. VCF/BCF generated by the new
samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
Single Individual Haplotyping (SIH) is added as an experimental feature. It
originally aims to produce haploid consensus from fosmid pool sequencing, but
also works with short-read data. For short reads, phased blocks are usually too
short to be useful in many applications, but they can help to rule out part of
SNPs close to INDELs or between copies of CNVs.
Other notable changes in samtools:
* Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
calling. This reduces the power but improves specificity.
* Improved sorting order checking in indexing. Now indexing is the preferred way
to check if a BAM is sorted.
* Added a switch `-E' to mpileup and calmd. This option uses an alternative way
to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
a little loss in specificity.
* Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
* Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
* Added `mpileup -S' to compute per-sample strand bias P-value.
* Added `mpileup -G' to exclude read groups in variant calling.
* Fixed segfault in indel calling related to unmapped and refskip reads.
* Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
genotypes for longer short INDELs, typically over 10bp.
* Fixed a bug in tview on big-endian machines.
* Fixed a very rare memory issue in bam_md.c
* Fixed an out-of-boundary bug in mpileup when the read base is `N'.
* Fixed a compiling error when the knetfile library is not used. Fixed a
library compiling error due to the lack of bam_nt16_nt4_table table.
Suppress a compiling warning related to the latest zlib.
Other notable changes in bcftools:
* Updated the BCF spec.
* Added the `FQ' VCF INFO field, which gives the phred-scaled probability
of all samples being the same (identical to the reference or all homozygous
variants). Option `view -f' has been dropped.
* Implemented "vcfutils.pl vcf2fq" to generate a consensus sequence
similar to "samtools.pl pileup2fq".
* Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
spec. Dropped bcf-fix.pl.
* Output bcftools specific INFO and FORMAT in the VCF header.
* Added `view -s' to call variants from a subset of samples.
* Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
custom fields are still unparsed and will be stored as a missing value.
* Fixed a minor bug in Fisher's exact test; the results are rarely affected.
(0.1.13: 1 March 2011, r926:134)
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