ANGSD/angsd

Issues

• bcf output file with "." at QUAL column

  #630 opened 20 days ago by martaolmu
  0

• https://www.popgen.dk/angsd/ is down

  #629 opened a month ago by silviagenome
  0

• bcf file doesn't open

  #628 opened a month ago by renatasoar3s
  0

• Killed

  #625 opened 3 months ago by isnmn
  1

• SAF file out of sync

  #627 opened 2 months ago by JoaoNunes15
  0

• empty output files

  #581 opened a year ago by Sven-Winter
  29

• Problems with unsorted saf file chromoname

  #626 opened 3 months ago by MboiTui
  1

• -argument is unknown will exit

  #624 opened 3 months ago by MboiTui
  1

• estAvgError.R script error

  #623 opened 3 months ago by lakshsesh97
  0

• 0 sites retained after filtering when using -sites

  #622 opened 3 months ago by henriquebatalha
  1

• Length of fastafile vs length of chr in BAM header

  #614 opened 6 months ago by pedrosenna
  1

• angsd: realloc() error

  #621 opened 3 months ago by iremdnzl
  0

• merging binary all 10 log genotype likelihood

  #620 opened 4 months ago by elenaasensimartinez
  0

• Number of numbers output by realSFS

  #619 opened 4 months ago by Erikacj
  1

• Missing windows in thetaStat

  #618 opened 4 months ago by jbruxaux
  0

• [loadChr] Error loading fasta info from chr

  #617 opened 5 months ago by dlema82
  0

• Population level theta with saf2theta

  #616 opened 6 months ago by jmhallas
  0

• -nan in Watterson / Pairwise position calculation.

  #606 opened 6 months ago by jmhallas
  2

• Contamination test, Error in dimnames(x)

  #615 opened 6 months ago by asli1-han
  0

• problems with estAvgError.R

  #613 opened 7 months ago by OthmanSN
  1

• How to check the convergence of results of realSFS?

  #593 opened a year ago by ChenJuiYANG
  1

• Problem computing cdf for chiseq, input is NaN, will exit

  #607 opened 9 months ago by stuartwillis
  3

• Segmentation Fault

  #612 opened 7 months ago by ciselkemahli
  1

• Help with glf file - corrupt?

  #587 opened a year ago by Erikacj
  5

• In version 0.934 how to convert haplo to tped? haploToPlink command no longer works

  #611 opened 7 months ago by cls83cam
  0

• Getting allele frequencies for different populations cutting a beagle file or using a -sites file?

  #610 opened 8 months ago by cleivama
  0

• -doBcf output corrupted?

  #600 opened 10 months ago by RyanEckert
  1

• SNP weights from covariance matrix

  #605 opened 9 months ago by Tannervanorden
  1

• ANGSD to calculate theta, is the result calculated log with 10 as the base or log with e as the base.

  #609 opened 9 months ago by mxt2022202059
  0

• Calculating folded SFS to account for highly polymorphic regions

  #608 opened 9 months ago by space-beaver
  0

• Filtering for LD with -sites

  #579 opened a year ago by RachelxGray
  2

• -doasso -yBin

  #604 opened 10 months ago by krcorder
  0

• Segmentation fault with error estimation using -doError

  #603 opened 10 months ago by jcaccavo
  0

• 2d folded sfs how to?

  #599 opened a year ago by darijajosic
  1

• Number of sites retained after filtering

  #602 opened 10 months ago by shuya099
  0

• Using results of error estimation

  #601 opened 10 months ago by jcaccavo
  0

• realSFS saf2theta output (out.thetas.idx) positions out of order

  #598 opened a year ago by slcapel
  1

• Uniable to print sad.idx files

  #597 opened a year ago by lpabonv
  0

• thetaStat：How can the tW and tP results be explained

  #594 opened a year ago by yangwukaidi
  1

• Unable to change the random seed for haploid genotype calling with doCounts/dohaplocall?

  #596 opened a year ago by TaurVil
  0

• The order of multi-sfs results

  #595 opened a year ago by ChenJuiYANG
  0

• Corrupted saf files were produced with multi-threads

  #592 opened a year ago by ChenJuiYANG
  0

• problems with estAvgError.R

  #591 opened a year ago by Tannervanorden
  0

• Determine missingness by sample from a beagle file or binary glf file generated by angsd?

  #589 opened a year ago by BKrek89
  0

• Association test stops after chromosome 1

  #588 opened a year ago by Erikacj
  1

• realSFS is OOM killed

  #584 opened a year ago by billiemaguire
  0

• ANGSD stuck while processing vcf file subset

  #585 opened a year ago by ThibauldMichel
  0

• Angsd gets stuck in the same genomic region in independent runs

  #583 opened a year ago by hyperoplus
  0

• Inbreeding, HWE and SFS for heterozygosity

  #580 opened a year ago by irbinveliz
  1

• Transitions not removed by -noTrans

  #582 opened a year ago by OKersten
  0