Ecosyste.ms: Issues

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GitHub / vibansal/HapCUT2 issues and pull requests

#131 - Convert block file to vcf after pruning

Issue - State: open - Opened by pdimens over 1 year ago - 1 comment

#130 - About maximum insert size of Hi-C data

Issue - State: closed - Opened by Yutang-ETH over 1 year ago - 2 comments

#129 - Merge vcf when combine HiC+HiFi?

Issue - State: closed - Opened by miaoxm2 over 1 year ago - 1 comment

#127 - Error while running extractHAIRS

Issue - State: open - Opened by uncleflybfchen over 2 years ago

#126 - Prevent a segfault error heuristically

Pull Request - State: open - Opened by pintomollo over 2 years ago

#125 - docs fix

Pull Request - State: closed - Opened by soymintc over 2 years ago - 1 comment

#123 - Feature/newer gcc compat

Pull Request - State: closed - Opened by snehring almost 3 years ago

#122 - There is a bit of confusion about the hic model

Issue - State: closed - Opened by YilinZhang449 about 3 years ago - 1 comment

#121 - double free or corruption (out)

Issue - State: open - Opened by tiffuhu about 3 years ago - 1 comment

#120 - error while loading shared libraries: libhts.so.3

Issue - State: open - Opened by sandipmkale about 3 years ago - 1 comment

#119 - is this tool suitable for Creating a phased VCF of proximal variants?

Issue - State: open - Opened by gudeqing over 3 years ago - 1 comment

#118 - Is there a docker image for this tool?

Issue - State: open - Opened by gudeqing over 3 years ago - 2 comments

#117 - split blocks

Issue - State: closed - Opened by ruqianl over 3 years ago - 4 comments

#116 - Possible to combine HiC, stLFR(10x) and nanopore long reads for phasing?

Issue - State: closed - Opened by melop over 3 years ago - 1 comment

#115 - Segfault on extracthairs

Issue - State: open - Opened by klannert over 3 years ago - 2 comments

#114 - Enable the use of the MI tag to detect molecules

Pull Request - State: closed - Opened by pontushojer over 3 years ago - 1 comment

#113 - Only a small part of SNPs can be phased

Issue - State: closed - Opened by JFF1594032292 almost 4 years ago - 1 comment

#112 - Question: support for de novo SNV/INDEL variants

Issue - State: closed - Opened by jbelyeu almost 4 years ago - 4 comments

#111 - Obtaining Phased Haplotypes

Issue - State: open - Opened by psur9757 almost 4 years ago - 5 comments
Labels: bug

#110 - HOMOZYGOUS_PRIOR too small

Issue - State: closed - Opened by jzhang-dev almost 4 years ago - 2 comments

#109 - HapCutToVcf result deal

Issue - State: open - Opened by LILIHAN-001 about 4 years ago

#108 - Only chr1 is phased.

Issue - State: closed - Opened by zhpn1024 about 4 years ago - 4 comments

#107 - More robust alignment index checking

Pull Request - State: closed - Opened by EdHarry over 4 years ago

#106 - which pipeline is good for calling variants?

Issue - State: closed - Opened by sunnycqcn over 4 years ago

#105 - HAPCUT2 error "segmentation fault (core dumped)"

Issue - State: closed - Opened by kisudsoe over 4 years ago - 1 comment

#104 - Make error (htslib not found)

Issue - State: closed - Opened by akijarl over 4 years ago - 2 comments

#103 - Phasing information from Supplementary alignments

Issue - State: closed - Opened by MaestSi over 4 years ago - 4 comments

#102 - Phase block contains variants from consecutive (different) chromosomes

Issue - State: closed - Opened by andremho over 4 years ago - 11 comments

#101 - run_hapcut2_fosmid_data.sh fails

Issue - State: closed - Opened by mathog over 4 years ago - 5 comments

#100 - Haplotype blocks between chromosomes

Issue - State: closed - Opened by conchoecia over 4 years ago - 1 comment

#99 - Conda version outdated

Issue - State: closed - Opened by StephenRicher over 4 years ago - 1 comment

#98 - HiC with HiC-Pro

Issue - State: closed - Opened by Yujiaxin419 over 4 years ago

#97 - Release 1.3 build warnings patch

Issue - State: closed - Opened by mathog almost 5 years ago - 3 comments

#95 - output vcf headers

Issue - State: closed - Opened by conchoecia almost 5 years ago - 1 comment

#94 - Hi-C with bwa mem -5SPM

Issue - State: closed - Opened by conchoecia about 5 years ago - 2 comments

#93 - Duitama et al. data download

Issue - State: closed - Opened by robinweide about 5 years ago - 2 comments

#92 - Valid [GT] accepted by extractHAIRS

Issue - State: closed - Opened by agroppi about 5 years ago - 2 comments

#91 - Outdated README

Issue - State: closed - Opened by FrickTobias about 5 years ago - 4 comments

#90 - 10X Genomics data in hapCUT2

Issue - State: open - Opened by burri-wildlight about 5 years ago - 8 comments

#89 - core segemntaion fault

Issue - State: closed - Opened by dhwani2410 about 5 years ago - 5 comments

#88 - multiple sequencing platform

Issue - State: closed - Opened by wyim-pgl about 5 years ago - 3 comments

#86 - Suggestion to make a new release

Issue - State: closed - Opened by marcelm over 5 years ago - 1 comment

#85 - Make Python utility scripts executable

Pull Request - State: closed - Opened by marcelm over 5 years ago

#84 - prune_haplotype.py format change?

Issue - State: closed - Opened by mdem7705 over 5 years ago - 6 comments

#83 - prune_haplotype.py got errors

Issue - State: closed - Opened by nganphanthi over 5 years ago

#82 - extractHAIRS for polyploids

Issue - State: open - Opened by sinamajidian over 5 years ago - 1 comment

#81 - hapcut2 what next

Issue - State: closed - Opened by rob123king over 5 years ago - 1 comment

#80 - Column order discrepancy between OS

Issue - State: closed - Opened by FrickTobias over 5 years ago - 4 comments

#79 - MEC score

Issue - State: closed - Opened by sinamajidian over 5 years ago - 4 comments

#78 - hapcut2 linkfragments error

Issue - State: open - Opened by jakobcmueller over 5 years ago

#77 - UnicodeDecodeError during linked_fragment_file generation

Issue - State: open - Opened by chunlinxiao over 5 years ago - 27 comments

#76 - HIC_repair.py error

Issue - State: closed - Opened by tommathers over 5 years ago - 2 comments

#75 - "Buffer overflow detected" when running HapCUT2

Issue - State: closed - Opened by olavurmortensen over 5 years ago - 11 comments

#74 - Leading white-space in "PD" format line

Issue - State: closed - Opened by olavurmortensen over 5 years ago - 2 comments

#73 - hapCUT2 running for excessive amount of time

Issue - State: closed - Opened by mdem7705 almost 6 years ago - 9 comments

#72 - HapCUT2 is dependent on pysam -- but which version?

Issue - State: closed - Opened by olavurmortensen almost 6 years ago - 2 comments

#71 - haplotyping polyploid genomes

Issue - State: closed - Opened by chklopp almost 6 years ago - 1 comment

#70 - Combining data from separate vcf files

Issue - State: closed - Opened by mdem7705 almost 6 years ago - 1 comment

#69 - *** Error in `extractHAIRS': free(): invalid size: 0x0000000001e34ac0 ***

Issue - State: closed - Opened by dhwani2410 almost 6 years ago - 6 comments

#68 - Installation error

Issue - State: closed - Opened by MeHelmy almost 6 years ago - 10 comments

#67 - Understanding HapCut2 blocks

Issue - State: closed - Opened by psur9757 almost 6 years ago - 6 comments

#65 - ExtractHAIRS error

Issue - State: closed - Opened by marizazh almost 6 years ago - 2 comments

#64 - extractHairs pointer error

Issue - State: closed - Opened by psur9757 almost 6 years ago - 3 comments

#63 - Invalid SNV confidence score on HAPCUT2 after extractHAIRS w/o filtering

Issue - State: closed - Opened by LillianZ almost 6 years ago - 1 comment

#62 - High missing SNPs for Pacbio

Issue - State: closed - Opened by sinamajidian almost 6 years ago - 3 comments

#61 - Short switch vs mismatch error

Issue - State: closed - Opened by cipher2k5 almost 6 years ago - 2 comments

#60 - read gzipped VCF files or exit with appropriate error message

Issue - State: closed - Opened by vibansal almost 6 years ago - 1 comment
Labels: enhancement

#59 - Make error (installation)

Issue - State: closed - Opened by ViriatoII about 6 years ago

#58 - Requirements for 10x barcoded reads

Issue - State: closed - Opened by olavurmortensen about 6 years ago - 1 comment

#57 - There No Exception and errors raised, but no output file

Issue - State: closed - Opened by jun3234 about 6 years ago - 4 comments

#56 - Invalid SNV confidence score

Issue - State: closed - Opened by YingYa over 6 years ago - 1 comment

#55 - bug found in extractHAIRS!

Issue - State: closed - Opened by yonghanyu over 6 years ago - 1 comment

#54 - Input format

Issue - State: closed - Opened by sinamajidian over 6 years ago - 2 comments

#53 - Problem in building

Issue - State: closed - Opened by sinamajidian over 6 years ago - 2 comments

#52 - Running HAPCUT2 after Canu

Issue - State: closed - Opened by psur9757 over 6 years ago - 9 comments

#51 - Run is taking longer than expected based on manuscript stats.

Issue - State: closed - Opened by conchoecia over 6 years ago - 7 comments

#50 - Confused about --indels

Issue - State: closed - Opened by conchoecia over 6 years ago - 2 comments

#49 - generate fasta of haplotype

Issue - State: closed - Opened by conchoecia over 6 years ago - 3 comments

#48 - error in extractHAIRS

Issue - State: closed - Opened by yaosl over 6 years ago - 2 comments

#47 - VCF files for de novo assembly

Issue - State: closed - Opened by mictadlo over 6 years ago - 1 comment

#46 - snakemake with 4 fastq files

Issue - State: closed - Opened by mictadlo over 6 years ago - 1 comment

#45 - extractHAIRS memory corruption (: 0x0000000048338980) in phasing Pacbio bam file

Issue - State: closed - Opened by penguab over 6 years ago - 7 comments

#44 - just 1 SNP?

Issue - State: closed - Opened by gilfunk over 6 years ago - 2 comments

#43 - options when combining Hi-C and Pacbio data (update recipe)

Issue - State: closed - Opened by rcosentino over 6 years ago - 2 comments

#42 - haplotype blocks no header after spliting with prune_haplotype.py

Issue - State: closed - Opened by linzhangTuesday almost 7 years ago - 2 comments

#41 - output column 2 and 3, what is the values "2" mean?

Issue - State: closed - Opened by Jeff-Liu9453 almost 7 years ago - 1 comment

#40 - The format of fragment file from extractHAIRS

Issue - State: closed - Opened by liangjiaoxue almost 7 years ago - 6 comments

#39 - empty result for pacbio data

Issue - State: closed - Opened by yilunhuangyue almost 7 years ago - 4 comments

#38 - Segmentation fault when running HAPCUT2

Issue - State: closed - Opened by maryawood almost 7 years ago - 8 comments

#37 - Can I use ./extractHARIS with multi-thread and how to do?

Issue - State: closed - Opened by jun3234 almost 7 years ago - 5 comments

#36 - Error while running extractHAIRS for human variance file

Issue - State: closed - Opened by qingpeng almost 7 years ago - 9 comments

#35 - extractHAIRS issue: useful fragments 0

Issue - State: closed - Opened by jkreinz almost 7 years ago - 1 comment

#33 - Request for suggestion on using HapCUT2 for phasing my genome of interest

Issue - State: closed - Opened by amit4mchiba almost 7 years ago - 6 comments

#30 - version and release software?

Issue - State: closed - Opened by nellore almost 7 years ago - 4 comments

#29 - output phased genotype likelihoods and allelic read depth (HapCUT2)

Issue - State: closed - Opened by vibansal about 7 years ago
Labels: enhancement

#27 - extracthairs for polyploid VCF

Issue - State: closed - Opened by vibansal about 7 years ago
Labels: enhancement