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• How to make a phylogenetic tree set in ASTRAL?
  How do I create a tree set in ASTRAL from several files? There are files for exons, introns and...
• Genotyped loci changed after imputation by Minimac4
  I ran Minimac4 to do imputation on the basis of ~750,000 loci that were genotyped. The reference ...
• XPEHH output file blank in SELSCAN
  I make a SELSCAN input file as .vcf file and a .map file with two population for XPEHH calculatio...
• View annotations in igv of bam file with multiple chromosomes
  I use IGV to view BAM files.  Most times I'm viewing single chromosome genomes.   When view singl...
• Cuffcompare : Why is the number of loci different from union of super-loci?
  I have a cuffcompare.stats file that contains : # Cuffcompare v2.2.1 | Command line was: ...
• How to divide a chromosome into arms and center?
  Hi all, I would like to get your input on how to make separate bed files of chromosome arms and ...
• vcftools discrepancy in mean depth values per site
  Dear all, I'm using VCFtools 0.1.17 to filter out loci with low coverage, this is the process: ...
• How Can I Make Sweeps Input File?
  dear all I am trying to find some way for make a input file of sweep 1.1, for detect selection s...
• Detection of loci under selection using Arlequin 3.5.2.2
  I am working with RADseq data and want to identify loci under selection using hierarchical island...
• The same loci for XP-EHH by Selscan
  Hello, I try to use selscan to compute the value of xpehh by selscan. But when I try to run it. I...
• How To Adjust The Chromosome Contigs Order
  When I run Baserecalibrator, my input reference file is genome.fa, my mapped file is K1_bam.marke...
• the function of readVCF in PopGenome R package
  Hello I'm using PopGenome R package to calculate Fst with vcf files. I met some problems during ...
• R/Circos, cannot make inter-chromosomal links to multiple chromosomes.
  I'm trying to make a synteny plot using R/Circos. I have two input files, one file with "cytogen...
• Matching files by chromosome during wdl scatter gather
  Hi, I'm trying to implement a polygenic score pipeline in WDL and I'm quite new to this pipeline...
• Using Plink to calculate LD between loci on different chromosomes
  I'm trying to calculate LD between loci on different chromosomes using plink on the 1000 genomes ...
• Bed File Coordinates
  Hi all, In a spreadsheet i have my list of rs# with their chromosomal number and locations. I wan...
• How to make a custom gtf or gff3 file with a list containing transcript loci
  Hi everyone, I have a text file containing thousands of tomato transcript loci , such as "SL2.50c...
• Arlequin Input Frequency Data
  Hi! I have frequency data for 50 biallelic loci and 500 samples in 3 populations and i can´t und...