# Uploaded samtools version 0.1.14-1.

[samtools.git] / NEWS

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+Beta release 0.1.14 (16 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release implements a method for testing associations for case-control
+data. The method does not call genotypes but instead sums over all genotype
+configurations to compute a chi^2 based test statistics. It can be potentially
+applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
+has not been evaluated on real data.
+
+Another new feature is to make X chromosome variant calls when female and male
+samples are both present. The user needs to provide a file indicating the
+ploidy of each sample.
+
+Other new features:
+
+ * Added `samtools mpileup -L' to skip INDEL calling in regions with
+   excessively high coverage. Such regions dramatically slow down mpileup.
+
+ * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
+   older which encode PL in a different way.
+
+(0.1.14: 16 March 2011, r930:163)
+
+
+
 Beta release 0.1.13 (1 March, 2011)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -56,7 +81,7 @@ 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 samei (identical to the reference or all homozygous
+   of all samples being the same (identical to the reference or all homozygous
    variants). Option `view -f' has been dropped.
 
  * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence