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UPDATES
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May 31 2017
fixed bug for overlapping PE reads (SINGLEREADS =1 option not working correctly, simple fix in hapfragments.c)
March 15 2016
modified extracthairs to handle = cigar operations.
July 2015
reorganized code: (1) extracthairs.c code is in separate directory 'parsebam'
(2) samtools-0.1.18 source code is part of repository to make it easy to compile code
code can be compiled by 'make all' in main HapCUT directory
March 26 2014
New version (0.7) available that is able to process PacBio data and tri-allelic variants. For PacBio data, quality values are sometimes not available
so the program assumes a constant sequencing error rate for all bases
Nov 11 2013
some bug fixes and updates for long read data
September 11 2013
New version of HapCUT (v.0.6) available for download. HapCUT can now generate haplotypes from fosmid pooled sequencing data
((Kitzman et al., Nature Biotech 2011)) and also from ligation based mate-pair sequencing data.
The code was uploaded to github for the first time.
July 17 2012
An updated version of HapCUT can be downloaded from attachments on main page (HAPCUT-v0.5.tar.gz). This includes pre-compiled binaries for linux and Mac OS.
May 1 2012
Fixed overlapping Paired-end issue: if a paired-end read covers the same variant twice, it is only considered once in the fragment. Code evaluated
on 1000 Genomes low coverage data.
April 19 2012
HapCUT now works with sorted BAM files and VCF files. It can also phase short insertion/deletion variants (indels). HapCUT is now 10-100 times faster than earlier versions.
July 05 2011
HapCUT has been extended to handle next-generation sequence data. HapCUT requires the reads for a diploid genome (aligned to a reference genome) in SAM/BAM format and a set of heterozygous variants. HapCUT uses the samtools API to parse bam files.
September 2007
The first version of HapCUT was implemented and the paper submitted to ECCB 2008