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2
votes
4
replies
581
views
VEP filtering query
ensembl-vep
4 months ago by prasundutta87 ▴ 660
1
vote
10
replies
1.2k
views
Coverage histogram query
Alignment
9 months ago by prasundutta87 ▴ 660
0
votes
2
replies
618
views
best practice to choose AF threshold based on population number
VCF AF allele-frequency
14 months ago by prasundutta87 ▴ 660
0
votes
0
replies
331
views
snpeff annotation query
snpeff structural-variation VCF
updated 14 months ago by 44k • written 14 months ago by ▴ 660
0
votes
2
replies
914
views
alternate allele frequency and minor allele frequency
rare common SNV SV VCF
18 months ago by prasundutta87 ▴ 660
4
votes
11
replies
11k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF snp
21 months ago by prasundutta87 ▴ 660
0
votes
0
replies
305
views
Tool for mode of inheritance based filtering for structural variants
StructuralVariants genotypes SNVs trio modeOfInheritance
2.1 years ago by prasundutta87 ▴ 660
2
votes
2
replies
2.9k
views
EPIC methylation manifest GRch38 query
methylation coordinates EPIC bedgraph CpG
updated 2.3 years ago by ▴ 10 • written 3.9 years ago by ▴ 660
0
votes
0
replies
429
views
query on filtering/dropping samples based on total reads (yield)
paired-end fastq Illumina
2.5 years ago by prasundutta87 ▴ 660
0
votes
1
reply
598
views
Structural variation nomenclature ambiguity
Structural_Variation
updated 2.6 years ago by ▴ 520 • written 2.6 years ago by ▴ 660
0
votes
2
replies
1.1k
views
Annotate Structural variants with population specific allele frequency values
allele Structural_variation VEP frequency VCF
2.7 years ago by prasundutta87 ▴ 660
3
votes
6
replies
1.4k
views
VEP chromosome name query
ensembl VCF annotation VEP
2.9 years ago by prasundutta87 ▴ 660
0
votes
0
replies
522
views
About Structural variation genotypes
variants Structural-variants variant-calling genotypes
updated 7 months ago by 44k • written 3.0 years ago by ▴ 660
2
votes
2
replies
1.5k
views
bcftools norm resulting in '*' in alternate allele
SNP bcftools VCF exome
3.3 years ago by prasundutta87 ▴ 660
1
vote
1
reply
1.3k
views
Using GRch38 (human genome) primary assembly for mapping long reads
assembly alignment
updated 3.3 years ago by 6.4k • written 3.3 years ago by ▴ 660
0
votes
0
replies
449
views
number of reads outside exonic regions in an exome sequencing experiment
exome next-gen sequencing
3.3 years ago by prasundutta87 ▴ 660
0
votes
0
replies
886
views
Using 1000 genomes phase 3 variants for BQSR
SNP next-gen snp GATK
3.3 years ago by prasundutta87 ▴ 660
4
votes
5
replies
857
views
Annotating variants using latest version fof the genome
SNP snp VCF
3.6 years ago by prasundutta87 ▴ 660
1
vote
1
reply
1.2k
views
rare SNP or SNV
snp snv
3.8 years ago by prasundutta87 ▴ 660
0
votes
0
replies
711
views
find tabix version
tabix software VCF
3.8 years ago by prasundutta87 ▴ 660
0
votes
4
replies
975
views
methylation % calculation for targeted region
methylation
3.9 years ago by prasundutta87 ▴ 660
0
votes
2
replies
2.1k
views
query regarding using manifest and annotation in Minfi (EPIC Methylation array analysis)
R Minfi EPIC array Methylation
updated 3.1 years ago by • 0 • written 4.0 years ago by ▴ 660
1
vote
2
replies
781
views
array jobs accessing one binary in population genetics software
population genetics software SGE
updated 4.1 years ago by 82k • written 4.1 years ago by ▴ 660
1
vote
10
replies
3.2k
views
illumina sequencing dual index query
sequencing
4.3 years ago by prasundutta87 ▴ 660
0
votes
1
reply
1.8k
views
soft-clipping during alignment and variant calling query
BWA-MEM GATK variant calling alignment
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 660
0
votes
1
reply
1.7k
views
SnpEff using -onlyprotein option (meaning-Only use protein coding transcripts)
RNA-Seq SNP gene software error
updated 4.6 years ago by ★ 1.5k • written 7.2 years ago by ▴ 660
0
votes
0
replies
1.1k
views
candidate region selection in an XP-EHH analysis
SNP XP-EHH
updated 4.8 years ago by 20 • written 5.2 years ago by ▴ 660
3
votes
3
replies
1.7k
views
allele specific expression (ASE) reference ratio plot query
RNA-Seq allele-specific expression SNP
4.9 years ago by prasundutta87 ▴ 660
1
vote
2
replies
2.7k
views
variant calling using reference transcriptome
RNA-Seq SNP reference transcriptome
updated 5.0 years ago by ▴ 10 • written 7.2 years ago by ▴ 660
0
votes
0
replies
1.0k
views
finding out SNPs from SNVs and breed specific SNPs
SNP SNV
updated 5.0 years ago by 20 • written 5.1 years ago by ▴ 660
1
vote
2
replies
1.5k
views
outliers in XP-EHH
population genetics outliers XP-EHH
5.2 years ago by prasundutta87 ▴ 660
7
votes
5
replies
4.8k
views
Difference between Private SNPs and Singleton SNPs
SNPs GATK variant calling SNP population genetics
5.3 years ago by prasundutta87 ▴ 660
0
votes
0
replies
5.6k
views
Correct way to report variant statistics from bcftools stats report
SNP variants statistics bcftools
5.3 years ago by prasundutta87 ▴ 660
5
votes
3
replies
1.1k
views
some good practices doubts
alignment gene variant calling
updated 5.4 years ago by 20 • written 6.5 years ago by ▴ 660
4
votes
9
replies
2.2k
views
no gene_id for tRNA in GFF3
annotation GFF3 GTF
5.6 years ago by prasundutta87 ▴ 660
0
votes
0
replies
1.1k
views
runtime error in LDhat
genome snp LDhat population genetics
5.6 years ago by prasundutta87 ▴ 660
0
votes
6
replies
1.7k
views
Filtering results difference amongst VCF files
SNP filtering GATK variants
5.6 years ago by prasundutta87 ▴ 660
0
votes
0
replies
1.5k
views
lookup table for LDhat
population genetics ldhat software
5.7 years ago by prasundutta87 ▴ 660
2
votes
2
replies
4.3k
views
PCA implementation in plink
Plink PCA population
updated 5.8 years ago by 10k • written 5.8 years ago by ▴ 660
0
votes
2
replies
863
views
query on a pre-process step involving GFF3
GFF3 annotation
5.8 years ago by prasundutta87 ▴ 660
1
vote
2
replies
1.2k
views
some questions on GFF3
GFF GTF annotation
5.8 years ago by prasundutta87 ▴ 660
1
vote
2
replies
2.6k
views
gffread query for gff to gtf conversion
GFF GTF annotation software
5.8 years ago by prasundutta87 ▴ 660
11
votes
5
replies
8.8k
views
HISAT2 MAPQ scoring scheme
alignment
5.8 years ago by prasundutta87 ▴ 660
0
votes
4
replies
948
views
sanity check methods for checking genome assembly coordinate changes
assembly genome sequence
5.8 years ago by prasundutta87 ▴ 660
3
votes
6
replies
1.2k
views
variant calling after reference genome is updated
SNP variant calling WGS
5.9 years ago by prasundutta87 ▴ 660
4
votes
14
replies
4.8k
views
Strategy in WGS variant calling using GATK (CombineGVCF step)
snp variant calling GATK WGS
6.1 years ago by prasundutta87 ▴ 660
0
votes
4
replies
1.1k
views
addressing software versions
best practices gatk software error
6.3 years ago by prasundutta87 ▴ 660
8
votes
10
replies
12k
views
fastqc adapter content
sequencing fastqc quality control
updated 6.3 years ago by 142k • written 6.3 years ago by ▴ 660
0
votes
3
replies
1.4k
views
heterozygosity during variant calling in a non-model organism such as Bubalus Bubalis
next-gen sequencing DNA-seq SNP
6.3 years ago by prasundutta87 ▴ 660
0
votes
6
replies
2.3k
views
excessive loading time for VCF files in IGV
snp visualization IGV
6.5 years ago by prasundutta87 ▴ 660
63 results • Page 1 of 2
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