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1
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6
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Generate VCF version 4.1 using GATK version 4
gatk4.0 vcf4.1
14 months ago by taniamahmood38 ▴ 50
3
votes
8
replies
1.2k
views
Which gatk version generates VCF version 4.1
vcf_v4.1 gatk
14 months ago by taniamahmood38 ▴ 50
0
votes
5
replies
1.1k
views
Error: ##fileformat=VCFv4.2 does not exist
Pharmcat VCF
updated 15 months ago by ▴ 480 • written 15 months ago by ▴ 50
0
votes
3
replies
1.8k
views
How to unzip a file with .bgz extention
.bgz unzip
updated 15 months ago by 142k • written 15 months ago by ▴ 50
0
votes
7
replies
1.1k
views
Issue with VCF format while using Pharmcat
Pharmcat VCF
15 months ago by taniamahmood38 ▴ 50
1
vote
3
replies
1.1k
views
Encountering error while using sudo apt-get update command
ubuntu offtopic
updated 18 months ago by 54k • written 18 months ago by ▴ 50
2
votes
2
replies
2.5k
views
How to install latest version of bcftools on ubuntu?
bcftools ubuntu bcftools1.16
updated 11 months ago by 43k • written 18 months ago by ▴ 50
0
votes
0
replies
299
views
Pool-HMM formula
Pool-HMM Python_program
19 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
314
views
Visualization of Pool-HMM results
Pool-HMM graphs
20 months ago by taniamahmood38 ▴ 50
0
votes
4
replies
772
views
Fastq to Fasta format
galaxy fastq fasta
20 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
292
views
How to calculate per site transition probability between hidden states.
-kargument pool-HMM
22 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
304
views
Require DH script
DH TajimasD H-statistics
23 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
363
views
Is Tajima's Pi and Wattersons Theta site frequency spectrum statistics?
TajimasD WattersonsTheta
23 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
371
views
Require combine script of Tajima'sD and Fay and Wu's H stats
H-statistics TajimasD
23 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
419
views
Require composite script of Hp and ROH statistics
ROH Pooled-heterozygosity github script
23 months ago by taniamahmood38 ▴ 50
0
votes
4
replies
700
views
How to convert VCF into hapmatrix format?
popseq hapmatrix vcf
24 months ago by taniamahmood38 ▴ 50
1
vote
4
replies
721
views
How to generate bam to vcf containing ancestral allele (AA) information?
ancestral_allele vcf bam
updated 24 months ago by 43k • written 24 months ago by ▴ 50
0
votes
0
replies
461
views
Understanding the output generated using rehh package
sfs Rehh
24 months ago by taniamahmood38 ▴ 50
2
votes
4
replies
1.5k
views
How to add the ancestral allele (AA) information in a vcf file?
AA_tag vcf
24 months ago by taniamahmood38 ▴ 50
0
votes
0
replies
316
views
Issue in computing the site frequency spectrum statistics using Rehh package
Rehh R
2.0 years ago by taniamahmood38 ▴ 50
2
votes
2
replies
752
views
Error in mapply(function(x, y)
rehh R
2.1 years ago by taniamahmood38 ▴ 50
0
votes
0
replies
339
views
Convert pileup file to genetic map file
genetic_map pileup .map
2.1 years ago by taniamahmood38 ▴ 50
2
votes
4
replies
770
views
Problem assigning read group to a sample
RG_tag popbam bam pooled-seq
2.1 years ago by taniamahmood38 ▴ 50
2
votes
4
replies
796
views
popbam: command not found
popbam
2.1 years ago by taniamahmood38 ▴ 50
1
vote
2
replies
633
views
How to add the PO tag in BAM file
PO_tag BAM POPBAM
2.1 years ago by taniamahmood38 ▴ 50
1
vote
2
replies
698
views
How to add @RG tags in vcf file?
vcf H_statistics POPBAM
updated 2.1 years ago by 161k • written 2.1 years ago by ▴ 50
0
votes
0
replies
298
views
How to resolve IndexError: too many indices for array?
pool-HMM python pooled-seq
2.1 years ago by taniamahmood38 ▴ 50
0
votes
0
replies
315
views
-p argument in freebayes for pooled sample
freebayes variant-calling pool-seq vcf
updated 7 months ago by 43k • written 2.1 years ago by ▴ 50
0
votes
2
replies
503
views
Error in polymutt2 tool compilation
argument.h vcf2map polymutt2
2.1 years ago by taniamahmood38 ▴ 50
1
vote
2
replies
465
views
Error: Could not open the input file
linux samtools pool-HMM
updated 11 months ago by 43k • written 2.1 years ago by ▴ 50
1
vote
2
replies
889
views
ImportError: cannot import name expm3
linuxOS Pool-HMM SciPy python2
2.1 years ago by taniamahmood38 ▴ 50
0
votes
0
replies
266
views
Issue with .map file generated using Plink software
genetic_map linuxOS .map_file Plink
2.1 years ago by taniamahmood38 ▴ 50
2
votes
6
replies
1.2k
views
Plant de novo genome assembly of illumina reads on linux
de_novo_genome_assembly linux plant_illumina_data
2.3 years ago by taniamahmood38 ▴ 50
0
votes
0
replies
1.3k
views
ImportError: cannot import name 'ft2font' from partially initialized module 'matplotlib'
bcftools matplotlib roh plot-roh.py
updated 11 months ago by 43k • written 2.3 years ago by ▴ 50
2
votes
2
replies
750
views
How to resolve the warning message in detectRUNS on R software
bcftools detectRUNS roh R
updated 11 months ago by 43k • written 2.3 years ago by ▴ 50
0
votes
0
replies
353
views
How to make Genetic map file required by bcftools
bcftools genetic-map roh
updated 11 months ago by 43k • written 2.3 years ago by ▴ 50
0
votes
0
replies
457
views
BCFtools roh analysis: Number of --estimate-AF samples: 0
bcftools roh AF
updated 11 months ago by 43k • written 2.3 years ago by ▴ 50
0
votes
2
replies
1.2k
views
libvcflib-tools error: Unable to correct problems, you have held broken packages
vcflib ubuntu20.04 libvcflib-tools
2.3 years ago by taniamahmood38 ▴ 50
2
votes
5
replies
1.5k
views
Selscan: ERROR: Alleles must be coded 0/1 only.
VCF nsl Selscan
2.4 years ago by taniamahmood38 ▴ 50
0
votes
0
replies
1.0k
views
A USER ERROR has occurred: no positional argument is defined for this tool.
GATK4 HaplotypeCaller BAM
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 50
0
votes
0
replies
524
views
GEMINI (GEnome MINIng) inheritance pattern command warning no affecteds in family 0
ubuntu GEnomeMINIng gemini
3.1 years ago by taniamahmood38 ▴ 50
1
vote
2
replies
1.0k
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
3.2 years ago by taniamahmood38 ▴ 50
1
vote
2
replies
988
views
Number of upregulated and downregulated genes from counts matrix
RNA-Seq DEGs up and downregulated genes
3.2 years ago by taniamahmood38 ▴ 50
2
votes
4
replies
1.3k
views
Converting a BAM/VCF into genetic recombination map tsv file
.tsv file format --GeneMap SelScan BAM/VCF
3.3 years ago by taniamahmood38 ▴ 50
10
votes
15
replies
2.3k
views
Convert BCF to BAM
BCF to BAM Linux Ubuntu terminal Command line
updated 4.1 years ago by • 0 • written 4.3 years ago by ▴ 50
1
vote
2
replies
757
views
Split synchronized file
sync file popoolation2 tool ubuntu
4.3 years ago by taniamahmood38 ▴ 50
46 results • Page 1 of 1
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