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Showing top results for tag: vcf • reset
3
votes
4
replies
351
views
Identifying Runs of Homozygosity and Inbreeding Coefficient from VCF File
SNP vcf genomics
updated 6 days ago by 44k • written 7 days ago by ▴ 10
0
votes
0
replies
170
views
how to convert hapmap genotype files (hmp.txt) to VCF format in Linux env.t?
snp vcf hapmap
updated 6 days ago by 44k • written 6 days ago by • 0
2
votes
1
reply
189
views
variant calling through gatk
variant-calling vcf workflow gatk
7 days ago by ashaneev07 ▴ 40
0
votes
2
replies
230
views
intersection of vcf files with bcf isec - no header
isec bcftools vcf
10 days ago by jasminestaples1 • 0
0
votes
0
replies
202
views
IGV - Load custom variant track
vcf igv react
20 days ago by sadapas • 0
0
votes
2
replies
316
views
Split vcf file to fit tbi requirements
snp HaplotypeCaller vcf gatk
17 days ago by cassandriatayfernandez • 0
0
votes
1
reply
252
views
co-occurrence matrix from my VCF file
co-occurrence vcf
updated 22 days ago by • 0 • written 23 days ago by • 0
0
votes
0
replies
187
views
Query regarding interpretation of VCF from variant calling (SVs) using vg giraffe workflow
pangenome giraffe vcf vg
22 days ago by s_135 ▴ 10
0
votes
1
reply
221
views
Identifying true variants between two strains despite low coverage
VCF bcftools mpileup variant-calling
updated 24 days ago by 44k • written 24 days ago by ▴ 20
1
vote
1
reply
274
views
Clinvar Filter
human genome vcf clinvar
updated 24 days ago by 146k • written 26 days ago by ▴ 10
0
votes
2
replies
381
views
Filtering the vcf file
vcf
26 days ago by trezini • 0
0
votes
3
replies
414
views
Understanding IGV
VCF IGV BAM WGS
updated 25 days ago by 146k • written 27 days ago by ★ 4.3k
0
votes
2
replies
331
views
bcftools/vt split multiallelics - split GT along with splitting multi-allelics
multiallelics decompose bcftools vcf vt
27 days ago by Ram 44k
1
vote
4
replies
460
views
VCF filter by read depth
VCF
updated 27 days ago by 44k • written 28 days ago by • 0
3
votes
4
replies
478
views
Cannot process a custom VCF file using bcftools
R bcftools VCF
updated 29 days ago by 164k • written 4 weeks ago by ▴ 10
0
votes
1
reply
252
views
How to compare SNPs in different population
SNPs genome VCF
updated 29 days ago by ★ 2.5k • written 4 weeks ago by • 0
0
votes
3
replies
321
views
How to convert CSV format to VCF using Python?
VCF CSV Python
updated 4 weeks ago by 44k • written 4 weeks ago by • 0
0
votes
0
replies
128
views
Significant difference in SNV count between replicates
VCF mutations WES SNV
4 weeks ago by dana • 0
0
votes
0
replies
176
views
VCF file missing MQRankSum and ReadPosRankSum for certain entries
snp vcf gatk
4 weeks ago by CRL-CHAR • 0
5
votes
12
replies
8.2k
views
how to run freebayes in multi-thread
VCF freebayes multi-thread
updated 4 weeks ago by 146k • written 5.7 years ago by ▴ 710
24
votes
11
replies
894
views
7 follow
Tool: A simple and lightweight tool for filtering csv file wirtten in Rust
gtf tab gff vcf csv
updated 4 weeks ago by 4.9k • written 5 weeks ago by ▴ 100
0
votes
1
reply
208
views
Convert vcf to specified input
snp vcf
updated 5 weeks ago by 164k • written 5 weeks ago by • 0
2
votes
3
replies
349
views
Structural Variants (SV) Manta output interpretation
manta vcf
updated 5 weeks ago by ▴ 290 • written 5 weeks ago by • 0
0
votes
0
replies
229
views
Merging Imputed VCF with Reference Panel VCF
VCF GLIMPSE Imputation
5 weeks ago by selplat21 ▴ 20
0
votes
1
reply
315
views
Integration of paired and single-end SRA
Paired-end Single-end VCF Resequencing
updated 6 weeks ago by 20k • written 6 weeks ago by ▴ 300
3
votes
2
replies
379
views
In Plink2, when converting a VCF file to bed format - how to retain original chromosome names?
plink2 vcf
7 weeks ago by rijan_dhakal2055 ▴ 10
0
votes
0
replies
230
views
1000 genomes's reference panel
vcf reference genetics
7 weeks ago by Hasan_Daaboul • 0
0
votes
0
replies
278
views
VCFTools Order of Flags Inquiry
vcf vcftools
updated 8 weeks ago by 9.8k • written 8 weeks ago by • 0
3
votes
1
reply
275
views
Why does the AD value of my VCF file display 3 values?
GATK vcf SnpEff
updated 8 weeks ago by 22k • written 8 weeks ago by ▴ 50
0
votes
1
reply
224
views
verifyBAMID in snakemake script error
config snakemake bam vcf verifyBAMID
updated 8 weeks ago by ▴ 850 • written 8 weeks ago by ▴ 210
0
votes
3
replies
348
views
Germline variant - should it be seen in the somatic vcf?
vcf somatic
updated 8 weeks ago by 44k • written 8 weeks ago by ▴ 190
1
vote
2
replies
366
views
How can I Obtain hg38 cancer mutation and variation files
VCF SNV variation mutation
updated 8 weeks ago by ▴ 90 • written 8 weeks ago by ▴ 90
0
votes
1
reply
343
views
Correct VCF header
VCF
updated 8 weeks ago by 44k • written 9 weeks ago by • 0
0
votes
0
replies
223
views
Handling FILTER Fields in VCF Metadata and Body
VCF
9 weeks ago by ManuelDB ▴ 110
1
vote
2
replies
329
views
Germline and somatic SNPs in same or different allele
germline vcf phasing somatic
8 weeks ago by Nacho del Valle • 0
2
votes
1
reply
343
views
Can I use snp data for iqtree?
alignment vcf iqtree variant-calling
updated 9 weeks ago by 44k • written 9 weeks ago by • 0
0
votes
2
replies
376
views
VCF files
GATK VCF homo-sapiens
updated 9 weeks ago by 88k • written 10 weeks ago by • 0
2
votes
4
replies
474
views
bcftools AA annotation failing
bcftools vcf ancestral-allele
9 weeks ago by Whirlingdaf ▴ 60
0
votes
1
reply
414
views
A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be us…
GATK VCF QD VariantRecalibrator
updated 10 weeks ago by ▴ 520 • written 10 weeks ago by • 0
0
votes
3
replies
371
views
VG - Verifying presence or absence of variants in Pangenome Graph
mutation variant pangenome vcf vg
updated 10 weeks ago by ▴ 640 • written 10 weeks ago by • 0
6
votes
11
replies
3.4k
views
Randomly select a number of variants and samples from a multi-sample VCF file (pVCF)
vcf pvcf
updated 9 weeks ago by 55k • written 22 months ago by ▴ 330
1
vote
2
replies
279
views
homo sapiens VCF
Alignment homo-sapiens vcf
updated 11 weeks ago by 44k • written 11 weeks ago by • 0
0
votes
1
reply
1.8k
views
Problems with overlapping variants in a vcf file
bcftools variant vcf
updated 11 weeks ago by 44k • written 3.8 years ago by ▴ 10
2
votes
1
reply
367
views
Removing / Excluding / Collapsing Overlapping Indels
bcftools genome vcf genotyping gatk
11 weeks ago by jon.klonowski ▴ 210
2
votes
3
replies
323
views
Manually creating a valid VCF File
vcf-validator vcf
updated 11 weeks ago by 5.8k • written 11 weeks ago by • 0
0
votes
1
reply
317
views
CLC Genomics workbench and dbSNP VCF import
VCF
updated 11 weeks ago by 146k • written 11 weeks ago by • 0
1
vote
2
replies
306
views
How to Detect Amino Acid Changes from a GATK VCF File and Reference Genome Using Code?
tabix codons vcf variants gatk
updated 12 weeks ago by 164k • written 12 weeks ago by ★ 4.3k
1
vote
10
replies
7.7k
views
6 follow
vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
vcftools vcf
updated 12 weeks ago by 44k • written 6.1 years ago by ▴ 10
1
vote
0
replies
224
views
dbNSFP in-silico predictor results counts not-equal to number to alternatives in vcf file
vcf
12 weeks ago by Lukas ▴ 130
9
votes
14
replies
1.2k
views
Proper reanotation of genepanel with snpEff and dbNSFP
vcf
12 weeks ago by Lukas ▴ 130
50 results • Page 1 of 1
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