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Showing top results for tag:
VCF
•
reset
0
votes
0
replies
49
views
VCF file missing MQRankSum and ReadPosRankSum for certain entries
snp
vcf
gatk
9 hours ago by
CRL-CHAR
• 0
5
votes
12
replies
8.0k
views
how to run freebayes in multi-thread
VCF
freebayes
multi-thread
updated 2 days ago by
GenoMax
145k • written 5.6 years ago by
marongiu.luigi
▴ 710
23
votes
11
replies
610
views
7 follow
Tool:
A simple and lightweight tool for filtering csv file wirtten in Rust
gtf
tab
gff
vcf
csv
updated 2 days ago by
Matthias Zepper
4.9k • written 3 days ago by
dwpeng
▴ 80
0
votes
1
reply
169
views
Convert vcf to specified input
snp
vcf
updated 5 days ago by
Pierre Lindenbaum
164k • written 5 days ago by
thomm80
• 0
2
votes
3
replies
241
views
Structural Variants (SV) Manta output interpretation
manta
vcf
updated 5 days ago by
DGTool
▴ 220 • written 5 days ago by
aleksandra.vitkovac97
• 0
0
votes
0
replies
205
views
Merging Imputed VCF with Reference Panel VCF
VCF
GLIMPSE
Imputation
9 days ago by
selplat21
▴ 20
0
votes
1
reply
277
views
Integration of paired and single-end SRA
Paired-end
Single-end
VCF
Resequencing
updated 10 days ago by
Brian Bushnell
20k • written 10 days ago by
reza
▴ 300
3
votes
2
replies
352
views
In Plink2, when converting a VCF file to bed format - how to retain original chromosome names?
plink2
vcf
20 days ago by
rijan_dhakal2055
▴ 10
0
votes
0
replies
218
views
1000 genomes's reference panel
vcf
reference
genetics
21 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
268
views
VCFTools Order of Flags Inquiry
vcf
vcftools
updated 24 days ago by
Medhat
9.8k • written 24 days ago by
S
• 0
3
votes
1
reply
251
views
Why does the AD value of my VCF file display 3 values?
GATK
vcf
SnpEff
updated 25 days ago by
Jeremy Leipzig
22k • written 25 days ago by
mgranada3
▴ 50
0
votes
1
reply
202
views
verifyBAMID in snakemake script error
config
snakemake
bam
vcf
verifyBAMID
updated 26 days ago by
Jesse
▴ 850 • written 27 days ago by
Peter Chung
▴ 210
0
votes
3
replies
320
views
Germline variant - should it be seen in the somatic vcf?
vcf
somatic
updated 26 days ago by
Ram
44k • written 27 days ago by
amy__
▴ 190
1
vote
2
replies
344
views
How can I Obtain hg38 cancer mutation and variation files
VCF
SNV
variation
mutation
updated 27 days ago by
gernophil
▴ 90 • written 29 days ago by
kabir.deb
▴ 90
0
votes
1
reply
307
views
Correct VCF header
VCF
updated 4 weeks ago by
Ram
44k • written 4 weeks ago by
ja569116
• 0
0
votes
0
replies
204
views
Handling FILTER Fields in VCF Metadata and Body
VCF
4 weeks ago by
ManuelDB
▴ 110
1
vote
2
replies
298
views
Germline and somatic SNPs in same or different allele
germline
vcf
phasing
somatic
4 weeks ago by
Nacho del Valle
• 0
2
votes
1
reply
269
views
Can I use snp data for iqtree?
alignment
vcf
iqtree
variant-calling
updated 4 weeks ago by
Ram
44k • written 4 weeks ago by
ylkim9
• 0
0
votes
2
replies
350
views
VCF files
GATK
VCF
homo-sapiens
updated 4 weeks ago by
Kevin Blighe
88k • written 6 weeks ago by
Sanazarghami4444
• 0
2
votes
4
replies
445
views
bcftools AA annotation failing
bcftools
vcf
ancestral-allele
5 weeks ago by
Whirlingdaf
▴ 60
0
votes
1
reply
387
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 5 weeks ago by
raphael.B
▴ 520 • written 5 weeks ago by
sam_brown_araujo
• 0
0
votes
3
replies
349
views
VG - Verifying presence or absence of variants in Pangenome Graph
mutation
variant
pangenome
vcf
vg
updated 5 weeks ago by
Jordan M Eizenga
▴ 620 • written 6 weeks ago by
nkls063408
• 0
6
votes
11
replies
3.3k
views
Randomly select a number of variants and samples from a multi-sample VCF file (pVCF)
vcf
pvcf
updated 5 weeks ago by
Michael
55k • written 20 months ago by
'
▴ 330
1
vote
2
replies
258
views
homo sapiens VCF
Alignment
homo-sapiens
vcf
updated 6 weeks ago by
Ram
44k • written 6 weeks ago by
Sanazarghami4444
• 0
0
votes
1
reply
1.7k
views
Problems with overlapping variants in a vcf file
bcftools
variant
vcf
updated 6 weeks ago by
Ram
44k • written 3.7 years ago by
Buxus
▴ 10
2
votes
1
reply
348
views
Removing / Excluding / Collapsing Overlapping Indels
bcftools
genome
vcf
genotyping
gatk
6 weeks ago by
jon.klonowski
▴ 210
2
votes
3
replies
301
views
Manually creating a valid VCF File
vcf-validator
vcf
updated 6 weeks ago by
Bastien Hervé
5.5k • written 6 weeks ago by
Sara
• 0
0
votes
1
reply
299
views
CLC Genomics workbench and dbSNP VCF import
VCF
updated 6 weeks ago by
GenoMax
145k • written 7 weeks ago by
むらい
• 0
1
vote
2
replies
276
views
How to Detect Amino Acid Changes from a GATK VCF File and Reference Genome Using Code?
tabix
codons
vcf
variants
gatk
updated 7 weeks ago by
Pierre Lindenbaum
164k • written 7 weeks ago by
DareDevil
★ 4.3k
1
vote
10
replies
7.6k
views
6 follow
vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
vcftools
vcf
updated 7 weeks ago by
Ram
44k • written 6.0 years ago by
mayara.salvian
▴ 10
1
vote
0
replies
209
views
dbNSFP in-silico predictor results counts not-equal to number to alternatives in vcf file
vcf
8 weeks ago by
Lukas
▴ 130
9
votes
14
replies
1.1k
views
Proper reanotation of genepanel with snpEff and dbNSFP
vcf
7 weeks ago by
Lukas
▴ 130
1
vote
2
replies
418
views
HTSLIB/VCF/C : get the first variant of each chromosome using htslib
htslib
vcf
c
8 weeks ago by
Pierre Lindenbaum
164k
4
votes
6
replies
481
views
Use LiftOver without knowing reference Fasta of used vcf file
vcf
updated 9 weeks ago by
GenoMax
145k • written 9 weeks ago by
Lukas
▴ 130
2
votes
4
replies
356
views
Replace SB flag by PASS in my VCF file
VCF
9 weeks ago by
ManuelDB
▴ 110
5
votes
12
replies
4.4k
views
10 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 9 weeks ago by
Etienne DVRK
• 0 • written 3.3 years ago by
pmc.sa
▴ 40
2
votes
1
reply
215
views
Filter vcf file by position AND alternative allele
bcftools
vcf
filter
updated 9 weeks ago by
zx8754
12k • written 9 weeks ago by
_quantum_girl_
▴ 40
1
vote
1
reply
298
views
Different Size VCF
GATK
VCF
compression
updated 10 weeks ago by
Pierre Lindenbaum
164k • written 10 weeks ago by
Sd
• 0
6
votes
5
replies
8.1k
views
9 follow
How to convert .vcf files into .csv?
vcf
csv
sql
python
vcftools
updated 10 weeks ago by
zx8754
12k • written 7.4 years ago by
feng9oly
• 0
2
votes
20
replies
1.4k
views
How to produce a single joint-called VCF file using as input three WGS samples (VCF,CRAM,FASTQ)
VCF
WGS
updated 9 weeks ago by
Ram
44k • written 11 weeks ago by
shwivel
• 0
0
votes
1
reply
248
views
how to count polymorphic snps in vcf file
vcf
updated 11 weeks ago by
Pierre Lindenbaum
164k • written 11 weeks ago by
26bhagwat
• 0
6
votes
11
replies
3.4k
views
6 follow
User friendly (visual&interactive) VCF/BCF mining tools (2021)
gui
vcf
updated 11 weeks ago by
venkat
▴ 10 • written 3.0 years ago by
William
★ 5.3k
2
votes
2
replies
277
views
Basics: How do I generate a VCF file from a genome and annotate it with Clinvar
VCF
Fastq
Clinvar
Annovar
updated 11 weeks ago by
colindaven
6.7k • written 11 weeks ago by
nanibito
▴ 10
0
votes
1
reply
229
views
VCF file GL field confusion
bcftools
format
VCF
genotype
specification
9 weeks ago by
mtrw85
▴ 10
0
votes
5
replies
564
views
How can I get an allele count table from a .vcf file?
GATK
calling
variant
vcf
updated 12 weeks ago by
Jeremy Leipzig
22k • written 12 weeks ago by
mrk
• 0
0
votes
1
reply
237
views
Remove variants from vcf file does not work
bcftools
vcf
vcftools
updated 12 weeks ago by
Ram
44k • written 12 weeks ago by
8armed
▴ 20
0
votes
2
replies
262
views
Count and filter sites with degenarate bases in VCF files
VCF
degenerate-bases
bisulfite-sequencing
updated 12 weeks ago by
Jeremy Leipzig
22k • written 12 weeks ago by
ja569116
• 0
0
votes
0
replies
142
views
Freebayes VCF Post-Calling Filter Optimization: Schizophrenia Gene Panel Insights
vcf
12 weeks ago by
Lukas
▴ 130
0
votes
2
replies
495
views
Nucleotide diversity and TajimaD from SNPs
GATK
TajimaD
vcf
updated 3 months ago by
Ram
44k • written 3 months ago by
BioD
• 0
4
votes
4
replies
582
views
Post-calling vcf filtration
vcf
3 months ago by
Lukas
▴ 130
50 results • Page
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Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
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