ANGSD/angsd issues and pull requests

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

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

#589 - Determine missingness by sample from a beagle file or binary glf file generated by angsd?

Issue - State: open - Opened by BKrek89 over 1 year ago

#588 - Association test stops after chromosome 1

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

#587 - Help with glf file - corrupt?

Issue - State: open - Opened by Erikacj over 1 year ago - 3 comments

#586 - [fix] Add howOften value check, add disable option

Pull Request - State: closed - Opened by isinaltinkaya over 1 year ago

#585 - ANGSD stuck while processing vcf file subset

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

#584 - realSFS is OOM killed

Issue - State: closed - Opened by billiemaguire over 1 year ago

#583 - Angsd gets stuck in the same genomic region in independent runs

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

#582 - Transitions not removed by -noTrans

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

#581 - empty output files

Issue - State: open - Opened by Sven-Winter over 1 year ago - 22 comments

#580 - Inbreeding, HWE and SFS for heterozygosity

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

#579 - Filtering for LD with -sites

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

#578 - What is PPmaf?

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

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

Pull Request - State: closed - Opened by isinaltinkaya over 1 year ago

#576 - Generating beagle or saf files from text glf input (`-glf10_text`) fails when contig names contain underscores.

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

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

Issue - State: open - Opened by marce-sarrias over 1 year ago - 3 comments

#574 - Calculate phenotypic variance explained by SNPs with GWAS output

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

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

Pull Request - State: closed - Opened by isinaltinkaya over 1 year ago

#572 - Genotype file does not contain missing data

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

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

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

#570 - PROBS at positions

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

#569 - [fix] Add VCF spanning deletion check

Pull Request - State: closed - Opened by isinaltinkaya over 1 year ago

#568 - visualization 2DSFS. plot2DSFS.R

Issue - State: open - Opened by yangwukaidi over 1 year ago - 2 comments

#567 - visualizing the 2D-SFS

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

#566 - Individual missingness and missing data

Issue - State: open - Opened by jmhallas over 1 year ago - 4 comments

#565 - Missing SNPS in doThetas Calculation

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

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

Issue - State: open - Opened by wul88 over 1 year ago - 2 comments

#563 - Installing ANGSD on M1x ventura 13.2

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

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

Pull Request - State: closed - Opened by isinaltinkaya over 1 year ago

#561 - 4D SFS segmentation fault

Issue - State: open - Opened by carolindahms over 1 year ago - 7 comments

#560 - cleaner error if no SNP sites

Pull Request - State: closed - Opened by abigailramsoe over 1 year ago

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

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

#558 - Problem with -doThetas

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

#557 - Error message 'Segmentation fault'

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

#556 - Discrete covariates in -doAsso

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

#555 - Thetas per population/genomic clusters, summarizing across chromosomes

Issue - State: open - Opened by akimmitt almost 2 years ago

#554 - Segmentation fault in msHOT2glf

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

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

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

#552 - ABBA-BABA_chimpHg19.fa.fai' looks older than corresponding fastafile

Issue - State: open - Opened by cyadrogarcia almost 2 years ago

#551 - Failed to open .bam file error

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

#550 - Killed

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

#549 - Is it possible to get population allele frequencies from PL values?

Issue - State: open - Opened by marcoesca almost 2 years ago

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

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

#547 - Permission denied after install

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

#546 - Merging beagle files

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

#545 - How to calculate allele frequencies from genotype likelihood (beagle file format)

Issue - State: open - Opened by Silvia-lme about 2 years ago

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

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

#543 - Is it possible to use a beagle input file to calculate HWE with ANGSD?

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

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

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

#541 - Mystery positions in GWAS

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

#540 - How to calculate the Global Population Branch Statistics (PBS) from per site PBS values

Issue - State: open - Opened by wul88 about 2 years ago - 1 comment

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

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

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

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

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

Issue - State: closed - Opened by jiangzy26 about 2 years ago

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

Issue - State: closed - Opened by jiangzy26 about 2 years ago

#535 - Compile problem at vcfReader

Issue - State: closed - Opened by dithiii about 2 years ago - 1 comment

#534 - Wrong header in realSFS fst index

Issue - State: open - Opened by beausoleilmo about 2 years ago - 4 comments

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

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

#532 - [chore] Merge master to branch

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

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

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

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

Issue - State: open - Opened by Raksha-95 about 2 years ago - 1 comment

#529 - Heterozygosity/genotype calling alternative allele frequencies

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

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

Pull Request - State: closed - Opened by isinaltinkaya about 2 years ago - 4 comments

#527 - [bug report] angsd sites breaks due to compiler flags

Issue - State: closed - Opened by isinaltinkaya about 2 years ago - 1 comment

#526 - Merge develop

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

#525 - Trying to run doAsso but receiving "Segmentation fault"

Issue - State: open - Opened by beausoleilmo about 2 years ago - 6 comments

#524 - Installation Error ::::: v0.938.

Issue - State: closed - Opened by g-pacheco about 2 years ago - 4 comments

#523 - Folded 2d SFS plot displays values beyond n1xn2 range

Issue - State: open - Opened by wul88 about 2 years ago - 9 comments

#522 - Estimating genotype likelihoods assuming inbreeding coefficient of 1

Issue - State: open - Opened by phillipsar2 about 2 years ago

#521 - Run restart + data conversion

Issue - State: closed - Opened by Imogen-D about 2 years ago - 2 comments

#520 - Empty Files: `counts.gz` and `pos.gz` ::::: v0.935 || v0.939

Issue - State: closed - Opened by g-pacheco about 2 years ago - 9 comments

#519 - Tajimas D calculation for site windows

Issue - State: closed - Opened by aguilar-gomez about 2 years ago - 2 comments

#518 - Fetch upstream

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

#517 - -dobcf --ignore-RG flag

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

#516 - bgzf_flush

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

#515 - angsd call snp vs gatk call snp

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

#514 - Fst value strongly affected by very low sample size, even with Bhatia -whichFst 1 option

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

#513 - Subsets of geno files

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

#512 - abbababa2 sample size discrepancy

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

#511 - [chore] Set crypto_try g++ to cxx; redirect output to /dev/null

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

#510 - realSFS command not found

Issue - State: closed - Opened by shailij246 over 2 years ago - 2 comments

#509 - File list reader needs to check for carriage returns in the file contents.

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

#508 - [feat,make] Add detect if -lcrypto is available on the system

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

#507 - [fixtest] Fix printing log to logfile in testBeagleReader

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

#506 - [fix,test] Fix printing log to logfile in testBeagleReader

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

#505 - [fix] Add -f to rm to fix error 1 in tests caused by rm exit 1

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

#504 - Overstimation of memory requirements

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

#503 - Installation issues

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

#501 - Why max thread cap?

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

#500 - [fix] unlogged banded SAF output in -doSaf 4 (beagle input); fix conflict

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

#499 - assoc5 Issue with weights being nan or inf

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

#498 - [fixleak]: Fix memory leaks in beagleReader

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

#486 - How do you unflatten a 2dSFS? Is Pop1 nrows or ncols in the matrix?

Issue - State: closed - Opened by TeresaPegan over 2 years ago - 8 comments

#480 - different number of loci for different runs with same script

Issue - State: closed - Opened by shri1984 over 2 years ago - 2 comments

#478 - error: ‘HTSCODECS_VERSION_TEXT’ undeclared

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

GitHub / ANGSD/angsd issues and pull requests