odelaneau shapeit4 issues

odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool

MIT License

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issues

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Error:[31mERROR: [0mCould not find conditioning haplotypes for [1032052] / check options --pbwt-* and --ibd2-*

#89 hangsuUNC opened 1 month ago
0
Reference dataset for Phase 3

#88 Anahit19 opened 11 months ago
0
error on bingraphsample

#87 taolincj closed 1 year ago
0
MacOS install error

#86 jpbreed90 opened 1 year ago
0
T2T chromosome maps?

#85 JosephLalli opened 1 year ago
0
Error: Underflow impossible to recover

#84 chantisakee opened 1 year ago
0
ERROR: Problem opening index file for hg19.fa

#83 Npaffen opened 1 year ago
2
Read-based phasing with underflow error

#82 Luker121 opened 1 year ago
0
Indel, CNV and Structural Variation (SV) in Shapeit4 phasing analysis

#81 Shicheng-Guo opened 1 year ago
2
AVX2 usage is determined at compile-time, not runtime

#80 pettyalex opened 1 year ago
0
Reading in files and genetic maps is done sequentially, and could be parallelized across threads

#79 pettyalex opened 1 year ago
1
Add a MacOS build: A couple of different options

#78 pettyalex opened 2 years ago
1
ERROR: Population based phasing for less than 20 individuals

#77 yaowei2010 opened 2 years ago
1
How to handle missing genotype

#76 rained1989 opened 2 years ago
1
Arch Linux package

#75 ramiromagno closed 1 year ago
1
Question about the static HTSlib library dependence

#74 ramiromagno closed 2 years ago
1
Illegal instruction (core dumped)

#73 Grelot opened 2 years ago
3
Cannot extract map files

#72 aritra90 opened 2 years ago
1
Scaffold and WhatsHap (physical and statistical phasing?)

#71 olekto opened 2 years ago
1
how to reduce the RAM when phasing a large cohort (~1200) of whole genome sequencing data with about 10Mb?

#70 xinkaitong opened 2 years ago
1
phasing without imputation

#69 Shicheng-Guo opened 2 years ago
2
Losing ~60% of variants from sequence data with SHAPEIT

#68 klmartinez opened 2 years ago
2
Minor Fixes

#67 rwk-unil opened 2 years ago
0
Getting shapeit4: command not found after successful installation

#66 rashindrie closed 2 years ago
2
shapeit4.2 - lto1: internal compiler error

#65 psammarco opened 2 years ago
5
haplotype inference for local region

#64 Shicheng-Guo opened 2 years ago
3
easy way to estimate required memory

#63 Shicheng-Guo opened 2 years ago
1
src/utils/otools.h:48:10: fatal error: htslib/hts.h: No such file or directory

#62 Shicheng-Guo closed 2 years ago
0
Weird and incorrect behavior when filling missing genotypes

#61 freeseek opened 2 years ago
2
Core dump on invoking on CentOS8

#60 brucedesertrat opened 2 years ago
1
Compilation Issue GCC 5.3.1

#59 denisemauldin opened 2 years ago
2
Keep old INFO and FORMAT field

#58 nickhir closed 2 years ago
1
Pedigree in shapeit4?

#57 tkn132 opened 3 years ago
3
SHAPEIT4 compilation error

#56 lyj95618 opened 3 years ago
3
Unable to install with conda

#55 tkn132 closed 3 years ago
1
free(): invalid pointer \n Aborted (core dumped)

#54 Bennouhan opened 3 years ago
2
Error: bcf_sr_set_threads was not declared in this scope; did you mean ‘bcf_sr_set_targets

#53 maojn opened 3 years ago
2
Unable to phase chromosome X of a cohort VCF with ~2,000 sample (updated)

#52 tedyun opened 3 years ago
4
Unable to phase chromosome X of a cohort VCF with ~2,000 sample

#51 tedyun closed 3 years ago
1
ERROR: Parsing line 0 : incorrect number of columns, observed: 1 expected: 3

#50 jessicahr closed 3 years ago
2
build issue in docker Unbuntu 20.04

#49 ghost closed 3 years ago
3
Change return type of merge

#48 cnettel opened 3 years ago
2
Buffer read overflow in pbwt_solver::sweep

#47 cnettel opened 3 years ago
0
'--pbwt-disable-init' not recognized

#46 mvaudel closed 3 years ago
2
shapeit fails with error message - Segmentation fault (core dumped)

#45 kvn95ss opened 3 years ago
25
Question on recombination maps

#44 BJWiley233 opened 3 years ago
2
Question in test folder hapmap for b37 chr20

#43 BJWiley233 opened 3 years ago
2
About including PS (phase set) information

#42 SIJAE-WOO closed 3 years ago
2
Segmentation fault (core dumped)

#41 SIJAE-WOO closed 3 years ago
1
missing genotypes in scaffold

#40 23andme-jaredo closed 3 years ago
2