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questions
1
vote
6
replies
1.5k
views
Generate VCF version 4.1 using GATK version 4
gatk4.0
vcf4.1
23 months ago by
taniamahmood38
▴ 60
3
votes
8
replies
1.7k
views
Which gatk version generates VCF version 4.1
vcf_v4.1
gatk
23 months ago by
taniamahmood38
▴ 60
0
votes
5
replies
1.6k
views
Error: ##fileformat=VCFv4.2 does not exist
Pharmcat
VCF
updated 2.0 years ago by
sbstevenlee
▴ 480 • written 2.0 years ago by
taniamahmood38
▴ 60
0
votes
3
replies
2.4k
views
How to unzip a file with .bgz extention
.bgz
unzip
updated 2.0 years ago by
GenoMax
149k • written 2.0 years ago by
taniamahmood38
▴ 60
0
votes
7
replies
1.5k
views
Issue with VCF format while using Pharmcat
Pharmcat
VCF
2.0 years ago by
taniamahmood38
▴ 60
1
vote
3
replies
1.5k
views
Encountering error while using sudo apt-get update command
ubuntu
offtopic
updated 2.2 years ago by
Michael
55k • written 2.2 years ago by
taniamahmood38
▴ 60
3
votes
2
replies
3.9k
views
How to install latest version of bcftools on ubuntu?
bcftools
ubuntu
bcftools1.16
updated 20 months ago by
Ram
44k • written 2.2 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
398
views
Pool-HMM formula
Pool-HMM
Python_program
2.4 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
411
views
Visualization of Pool-HMM results
Pool-HMM
graphs
2.4 years ago by
taniamahmood38
▴ 60
0
votes
4
replies
1.1k
views
Fastq to Fasta format
galaxy
fastq
fasta
2.4 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
389
views
How to calculate per site transition probability between hidden states.
-kargument
pool-HMM
2.6 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
407
views
Require DH script
DH
TajimasD
H-statistics
2.7 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
462
views
Is Tajima's Pi and Wattersons Theta site frequency spectrum statistics?
TajimasD
WattersonsTheta
2.7 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
481
views
Require combine script of Tajima'sD and Fay and Wu's H stats
H-statistics
TajimasD
2.7 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
527
views
Require composite script of Hp and ROH statistics
ROH
Pooled-heterozygosity
github
script
2.7 years ago by
taniamahmood38
▴ 60
0
votes
4
replies
959
views
How to convert VCF into hapmatrix format?
popseq
hapmatrix
vcf
2.7 years ago by
taniamahmood38
▴ 60
1
vote
4
replies
971
views
How to generate bam to vcf containing ancestral allele (AA) information?
ancestral_allele
vcf
bam
updated 2.7 years ago by
Ram
44k • written 2.7 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
587
views
Understanding the output generated using rehh package
sfs
Rehh
2.7 years ago by
taniamahmood38
▴ 60
2
votes
4
replies
2.0k
views
How to add the ancestral allele (AA) information in a vcf file?
AA_tag
vcf
2.7 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
403
views
Issue in computing the site frequency spectrum statistics using Rehh package
Rehh
R
2.8 years ago by
taniamahmood38
▴ 60
2
votes
2
replies
1.0k
views
Error in mapply(function(x, y)
rehh
R
2.8 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
446
views
Convert pileup file to genetic map file
genetic_map
pileup
.map
2.8 years ago by
taniamahmood38
▴ 60
2
votes
4
replies
1.0k
views
Problem assigning read group to a sample
RG_tag
popbam
bam
pooled-seq
2.8 years ago by
taniamahmood38
▴ 60
2
votes
4
replies
1.0k
views
popbam: command not found
popbam
2.8 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
853
views
How to add the PO tag in BAM file
PO_tag
BAM
POPBAM
2.8 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
937
views
How to add @RG tags in vcf file?
vcf
H_statistics
POPBAM
updated 2.8 years ago by
Pierre Lindenbaum
165k • written 2.8 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
394
views
How to resolve IndexError: too many indices for array?
pool-HMM
python
pooled-seq
2.9 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
432
views
-p argument in freebayes for pooled sample
freebayes
variant-calling
pool-seq
vcf
updated 16 months ago by
Ram
44k • written 2.9 years ago by
taniamahmood38
▴ 60
0
votes
2
replies
670
views
Error in polymutt2 tool compilation
argument.h
vcf2map
polymutt2
2.9 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
622
views
Error: Could not open the input file
linux
samtools
pool-HMM
updated 20 months ago by
Ram
44k • written 2.9 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
1.1k
views
ImportError: cannot import name expm3
linuxOS
Pool-HMM
SciPy
python2
2.9 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
354
views
Issue with .map file generated using Plink software
genetic_map
linuxOS
.map_file
Plink
2.9 years ago by
taniamahmood38
▴ 60
2
votes
6
replies
1.6k
views
Plant de novo genome assembly of illumina reads on linux
de_novo_genome_assembly
linux
plant_illumina_data
3.0 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
1.5k
views
ImportError: cannot import name 'ft2font' from partially initialized module 'matplotlib'
bcftools
matplotlib
roh
plot-roh.py
updated 20 months ago by
Ram
44k • written 3.0 years ago by
taniamahmood38
▴ 60
2
votes
2
replies
948
views
How to resolve the warning message in detectRUNS on R software
bcftools
detectRUNS
roh
R
updated 20 months ago by
Ram
44k • written 3.0 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
448
views
How to make Genetic map file required by bcftools
bcftools
genetic-map
roh
updated 20 months ago by
Ram
44k • written 3.0 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
575
views
BCFtools roh analysis: Number of --estimate-AF samples: 0
bcftools
roh
AF
updated 20 months ago by
Ram
44k • written 3.0 years ago by
taniamahmood38
▴ 60
0
votes
2
replies
1.4k
views
libvcflib-tools error: Unable to correct problems, you have held broken packages
vcflib
ubuntu20.04
libvcflib-tools
3.1 years ago by
taniamahmood38
▴ 60
2
votes
5
replies
2.0k
views
Selscan: ERROR: Alleles must be coded 0/1 only.
VCF
nsl
Selscan
3.1 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
1.3k
views
A USER ERROR has occurred: no positional argument is defined for this tool.
GATK4
HaplotypeCaller
BAM
updated 3.5 years ago by
Ram
44k • written 3.5 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
623
views
GEMINI (GEnome MINIng) inheritance pattern command warning no affecteds in family 0
ubuntu
GEnomeMINIng
gemini
3.9 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
1.2k
views
Script for XP-EHH, EHH and iHS tests and phasing vcf file that works on all chromosome concurrently
WGS
Pooled-Seq
XPEHH
EHH
iHS
3.9 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
1.2k
views
Number of upregulated and downregulated genes from counts matrix
RNA-Seq
DEGs
up and downregulated genes
4.0 years ago by
taniamahmood38
▴ 60
2
votes
4
replies
1.6k
views
Converting a BAM/VCF into genetic recombination map tsv file
.tsv file format
--GeneMap
SelScan
BAM/VCF
4.0 years ago by
taniamahmood38
▴ 60
10
votes
15
replies
2.8k
views
Convert BCF to BAM
BCF to BAM
Linux
Ubuntu terminal
Command line
updated 4.8 years ago by
rgsingleton
• 0 • written 5.0 years ago by
taniamahmood38
▴ 60
1
vote
2
replies
931
views
Split synchronized file
sync file
popoolation2 tool
ubuntu
5.0 years ago by
taniamahmood38
▴ 60
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