haplohseq identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample. Input to the software includes a VCF file of genotypes and estimated phased genotypes. The software produces a posterior probability file that includes probabilities of an allelic imbalance event for each heterozygous, polymorphic genomic site contained in the VCF file.
hapLOHseq has been developed for the detection of subtle allelic imbalance events from next-generation sequencing data. hapLOHseq is a sequencing-based extension of hapLOH (Vattathil and Scheet, Genome Research 2013), which is a method for the detection of subtle allelic imbalance events from SNP array data. hapLOHseq is capable of identifying events of 10 mega-bases or greater occurring in as little as 16% of the sample using exome sequencing data (at 80x) and 4% using whole genome se-quencing data (at 30x), far exceeding the capabilities of existing software.
hapLOHseq was developed by Anthony San Lucas and Paul Scheet with assistance from Jerry Fowler.
hapLOHseq is freely available with an MIT license. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Documentation is available at Integrative Cancer Genomics
Please register to obtain the hapLOHseq software.