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GitHub / ANGSD/angsd issues and pull requests

#656 - Minor points on installation

Issue - State: open - Opened by jinghuazhao 1 day ago

#653 - saf2theta realsfs.old error

Issue - State: open - Opened by dlema82 5 months ago

#652 - doIBS default -maxFreq argument removes all sites

Issue - State: open - Opened by alexpiper 5 months ago

#651 - vcf input with population info

Issue - State: open - Opened by Ida921 5 months ago

#650 - Issue in SNP calling

Issue - State: open - Opened by faizee-ali 6 months ago

#647 - Locating DSTAT.R

Issue - State: open - Opened by szitenberg 7 months ago

#644 - Calling pseudohaploid genotypes

Issue - State: open - Opened by jkimsis 8 months ago

#643 - install issues fPIE

Issue - State: closed - Opened by liushanlin 8 months ago

#640 - glfReader.cpp killed

Issue - State: open - Opened by masashi-S-suzie 9 months ago

#639 - installation - Error 127

Issue - State: open - Opened by juanfmasello 10 months ago

#636 - Expected and observed hets

Issue - State: open - Opened by ebutoto 11 months ago

#635 - covariates not used in association tests with .sample file.

Pull Request - State: open - Opened by RJDan 12 months ago

#633 - "allocate too much memory" realSFS FST

Issue - State: open - Opened by jmhallas 12 months ago

#630 - bcf output file with "." at QUAL column

Issue - State: open - Opened by martaolmu about 1 year ago

#629 - https://www.popgen.dk/angsd/ is down

Pull Request - State: closed - Opened by silviagenome about 1 year ago

#628 - bcf file doesn't open

Issue - State: open - Opened by renatasoar3s about 1 year ago

#627 - SAF file out of sync

Issue - State: open - Opened by JoaoNunes15 about 1 year ago

#626 - Problems with unsorted saf file chromoname

Pull Request - State: open - Opened by MboiTui about 1 year ago

#625 - Killed

Pull Request - State: open - Opened by isnmn over 1 year ago

#624 - -argument is unknown will exit

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

#623 - estAvgError.R script error

Issue - State: open - Opened by lakshsesh97 over 1 year ago

#621 - angsd: realloc() error

Issue - State: open - Opened by iremdnzl over 1 year ago

#620 - merging binary all 10 log genotype likelihood

Issue - State: open - Opened by elenaasensimartinez over 1 year ago

#619 - Number numbers output by realSFS

Pull Request - State: open - Opened by Erikacj over 1 year ago

#618 - Missing windows in thetaStat

Issue - State: open - Opened by jbruxaux over 1 year ago

#616 - Population level theta with saf2theta

Issue - State: open - Opened by jmhallas over 1 year ago

#615 - Contamination test, Error in dimnames(x)

Issue - State: open - Opened by asli1-han over 1 year ago

#614 - Length of fastafile vs length of chr in BAM header

Issue - State: open - Opened by pedrosenna over 1 year ago

#613 - problems with estAvgError.R

Issue - State: open - Opened by OthmanSN over 1 year ago

#612 - Segmentation Fault

Issue - State: open - Opened by ciselkemahli over 1 year ago

#606 - -nan in Watterson / Pairwise position calculation.

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

#590 - Makefile: specify version.h as a dependency of all object files

Pull Request - State: open - Opened by trofi about 2 years ago

#587 - Help with glf file - corrupt?

Issue - State: open - Opened by Erikacj about 2 years ago - 3 comments

#585 - ANGSD stuck while processing vcf file subset

Issue - State: open - Opened by ThibauldMichel about 2 years ago

#584 - realSFS is OOM killed

Issue - State: closed - Opened by billiemaguire about 2 years ago

#582 - Transitions not removed by -noTrans

Issue - State: open - Opened by OKersten about 2 years ago

#581 - empty output files

Issue - State: open - Opened by Sven-Winter about 2 years ago - 22 comments

#580 - Inbreeding, HWE and SFS for heterozygosity

Issue - State: open - Opened by irbinveliz about 2 years ago - 1 comment

#579 - Filtering for LD with -sites

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

#578 - What is PPmaf?

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

#577 - [fix] Add missing parenthesis to assert macro

Pull Request - State: closed - Opened by isinaltinkaya over 2 years ago

#575 - cannot convert vcf file to beagle binary format using the -vcf-gl option

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

#573 - [build] Remove install -D to support osx build

Pull Request - State: closed - Opened by isinaltinkaya over 2 years ago

#572 - Genotype file does not contain missing data

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

#571 - Number of sites for SFS, incl. multi-allelic ones

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

#570 - PROBS at positions

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

#569 - [fix] Add VCF spanning deletion check

Pull Request - State: closed - Opened by isinaltinkaya over 2 years ago

#568 - visualization 2DSFS. plot2DSFS.R

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

#567 - visualizing the 2D-SFS

Issue - State: closed - Opened by yangwukaidi over 2 years ago - 1 comment

#566 - Individual missingness and missing data

Issue - State: open - Opened by jmhallas over 2 years ago - 4 comments

#565 - Missing SNPS in doThetas Calculation

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

#564 - Find older version ANGSD0.922 from commit#

Issue - State: open - Opened by wul88 over 2 years ago - 2 comments

#563 - Installing ANGSD on M1x ventura 13.2

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

#562 - [fix][VCF,indel] Add check for deletion in alleles

Pull Request - State: closed - Opened by isinaltinkaya over 2 years ago

#561 - 4D SFS segmentation fault

Issue - State: open - Opened by carolindahms over 2 years ago - 7 comments

#560 - cleaner error if no SNP sites

Pull Request - State: closed - Opened by abigailramsoe over 2 years ago

#559 - [bug?] Angsd sets qual of first site to 0

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

#558 - Problem with -doThetas

Issue - State: open - Opened by MehrabChowdhury1 over 2 years ago - 3 comments

#557 - Error message 'Segmentation fault'

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

#556 - Discrete covariates in -doAsso

Issue - State: open - Opened by maehrlich1 over 2 years ago

#554 - Segmentation fault in msHOT2glf

Issue - State: open - Opened by niki3502 over 2 years ago

#553 - [bug?] Angsd fills GL tags of sites with missing GLs with 0s

Issue - State: open - Opened by isinaltinkaya over 2 years ago - 1 comment

#551 - Failed to open .bam file error

Issue - State: closed - Opened by staceyg947 over 2 years ago - 5 comments

#550 - Killed

Issue - State: open - Opened by iremdnzl over 2 years ago - 1 comment

#548 - Calculating Fst for windows with a fixed number of SNPs

Issue - State: open - Opened by EmilyPhelps over 2 years ago - 1 comment

#547 - Permission denied after install

Issue - State: open - Opened by Otorongo1 over 2 years ago - 3 comments

#546 - Merging beagle files

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

#544 - Issue with multi-threaded BCF input for SAF

Issue - State: open - Opened by malthesr almost 3 years ago

#542 - No data for chromoId=0 chromoname=... with -doFasta

Issue - State: open - Opened by beausoleilmo almost 3 years ago

#541 - Mystery positions in GWAS

Issue - State: closed - Opened by EmilyPhelps almost 3 years ago

#539 - [fix] Add -D__STDC_FORMAT_MACROS to FLAGS for C99

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

#538 - realSFS - homozygous for the alternative allele returns a zero value.

Issue - State: open - Opened by jcchacond almost 3 years ago - 3 comments

#537 - The reference or equations of Fst and theta pi

Issue - State: closed - Opened by jiangzy26 almost 3 years ago

#536 - Calculate PBS values based on more than three populations

Issue - State: closed - Opened by jiangzy26 almost 3 years ago

#535 - Compile problem at vcfReader

Issue - State: closed - Opened by dithiii almost 3 years ago - 1 comment

#534 - Wrong header in realSFS fst index

Issue - State: open - Opened by beausoleilmo almost 3 years ago - 4 comments

#533 - [fix]: Fix assert bug related to DNDEBUG flags #527

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

#532 - [chore] Merge master to branch

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

#531 - [fix]: Replace assert statements with aio assert

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

#530 - RealSFS Watterson's Theta, Issue with size of dimension

Issue - State: open - Opened by Raksha-95 almost 3 years ago - 1 comment

#529 - Heterozygosity/genotype calling alternative allele frequencies

Issue - State: open - Opened by Mvwestbury almost 3 years ago - 3 comments

#528 - [fix] Fix compiler flags related sites parsing issue, fixes #527

Pull Request - State: closed - Opened by isinaltinkaya almost 3 years ago - 4 comments