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0
votes
4
replies
9.4k
views
How to force merge a VCF files, for different samples?
vcf merge SNP genome
written 6.8 years ago by ★ 1.6k
3
votes
2
replies
5.8k
views
Calculate Allele balance by sample
Allele balance SNP RNA-Seq
updated 3.2 years ago by ▴ 130 • written 8.1 years ago by ★ 1.6k
1
vote
1
reply
922
views
Synonym gene names have some ambiguity. Is it a curation issue or something biological?
gene gene curation NCBI Ensembl
updated 5.6 years ago by 11k • written 6.2 years ago by ★ 1.6k
0
votes
1
reply
2.8k
views
How to prepare index/server for blat?
blat alignment index gfServer
updated 5.6 years ago by 43k • written 8.2 years ago by ★ 1.6k
8
votes
8
replies
11k
views
How to add custom fields to the VCF files?
vcf phasing SNP annotation manipulation
updated 5.6 years ago by ▴ 90 • written 7.6 years ago by ★ 1.6k
0
votes
0
replies
1.4k
views
Benchmarking datasets for Haplotype phasing
genome haplotype phasing shapeit NA12891
5.7 years ago by kirannbishwa01 ★ 1.6k
8
votes
8
replies
14k
views
STAR genome index with and/or with out *.gtf annotation
STAR gtf RNA-Seq alignment bowtie
updated 5.7 years ago by • 0 • written 7.9 years ago by ★ 1.6k
8
votes
8
replies
6.2k
views
Bam to fastq conversion is giving error?
bam fastq picard software error genome
updated 5.9 years ago by 20 • written 6.9 years ago by ★ 1.6k
0
votes
13
replies
2.7k
views
bcftools consensus not working when using -H flag
bcftools vcf software error reference genome
updated 5.9 years ago by 16k • written 5.9 years ago by ★ 1.6k
0
votes
0
replies
1.9k
views
GFF liftOver using CrossMap is failing.
software error Gff liftOver CrossMap
5.9 years ago by kirannbishwa01 ★ 1.6k
3
votes
1
reply
3.4k
views
Coverting missing sites to reference allele using Bcftools isn't working.
bcftools vcf software error genome genotype
updated 5.9 years ago by 16k • written 5.9 years ago by ★ 1.6k
2
votes
2
replies
1.7k
views
What is the structure of the data in Haplotype reference panel?
genome haplotype reference panels variants
6.1 years ago by kirannbishwa01 ★ 1.6k
21
votes
18
replies
21k
views
bcftools merge of multiple vcf produces duplicate records. How to solve the issue.
VCF vcf merge bcftools duplicate records variants
updated 6.1 years ago by 87k • written 6.1 years ago by ★ 1.6k
0
votes
0
replies
1.5k
views
Explanation of the markov chain in the given plot.
R python markov chain markov process plot
6.3 years ago by kirannbishwa01 ★ 1.6k
15
votes
21
replies
5.8k
views
Pysam is giving - ValueError: reference_id -1 out of range 0<=tid<65334. Any suggestions?
pysam sam bam reference_id
updated 6.3 years ago by 10k • written 7.9 years ago by ★ 1.6k
6
votes
4
replies
5.2k
views
How to update the INFO field of VCF after merging, subsetting?
vcf merge genome INFO vcftools
updated 6.3 years ago by ▴ 30 • written 6.3 years ago by ★ 1.6k
1
vote
1
reply
2.1k
views
Udpate the FILTER field in VCF to PASS if the variants is represented as true in another set of VCF?
vcf PASS SNP
updated 6.3 years ago by 161k • written 6.3 years ago by ★ 1.6k
20
votes
6
replies
4.8k
views
Some clarification on enrichment analyses and pathway analyses?
pathview R gene-enrichment RNA-Seq
updated 11 months ago by 43k • written 6.4 years ago by ★ 1.6k
4
votes
4
replies
2.8k
views
How to name the genome in karyoploteR ?
karyoploteR genome RNA-Seq software error
updated 6.5 years ago by ★ 3.4k • written 6.5 years ago by ★ 1.6k
0
votes
0
replies
1.6k
views
How to count the number of unique alignment in PE reads? How to account for unmapped mate?
bam count alignment genome
6.8 years ago by kirannbishwa01 ★ 1.6k
2
votes
15
replies
3.1k
views
How to do genome guided denovo assembly? If not, how to align the denovo assembled bam to a particular reference genome?
genome alignment Assembly allpathsLG paralogous
updated 6.9 years ago by 35k • written 6.9 years ago by ★ 1.6k
6
votes
6
replies
2.5k
views
How to select lines (filter) in vcf files that have same genotypes for all the samples?
vcf pyvcf genotype genome sequence
updated 6.9 years ago by 161k • written 6.9 years ago by ★ 1.6k
1
vote
6
replies
2.3k
views
How to find the sites/lines in vcf that are fixed for alleles in two different populations?
genome next-gen alleles vcf population genetics
6.9 years ago by kirannbishwa01 ★ 1.6k
5
votes
9
replies
5.0k
views
How to write the variant (allele) information back into a vcf file?
vcf SNP allele genome next-gen
updated 6.9 years ago by ★ 2.8k • written 7.0 years ago by ★ 1.6k
1
vote
0
replies
2.5k
views
How do I add/update the FORMAT field and it values in SAMPLE field?
software error vcf pyvcf python add_field
6.9 years ago by kirannbishwa01 ★ 1.6k
0
votes
2
replies
1.8k
views
How to select specific values (features and attributes) from gtf/gff file and convert it into table like data?
gtf gff features attributes
updated 7.0 years ago by 35k • written 7.0 years ago by ★ 1.6k
1
vote
1
reply
1.1k
views
Any opinions on the use of (or experience with) BWBBLE?
genome snp alignment sequence BWBBLE
7.0 years ago by kirannbishwa01 ★ 1.6k
2
votes
18
replies
2.0k
views
How to update the fileds in bedfiles (or dataframes) based on overlaps from between intervals of two bedfiles (dataframes)?
bedtools merge python gene_features update
7.0 years ago by kirannbishwa01 ★ 1.6k
2
votes
1
reply
3.1k
views
Which software can be used to extend the partially phased vcf from several different individuals (samples) to get an extend length haplotype?
vcf SNP genome haplotype phasing genotype phasing
7.0 years ago by kirannbishwa01 ★ 1.6k
3
votes
6
replies
3.4k
views
How to call genotype bases for all the samples in a vcf using for-loop?
pyvcf vcf snps GT software error
7.1 years ago by kirannbishwa01 ★ 1.6k
0
votes
0
replies
1.5k
views
How to separate the haplotype in a hybrid given phase states in two different blocks?
python haplotype vcf phasing SNP
7.2 years ago by kirannbishwa01 ★ 1.6k
0
votes
1
reply
1.6k
views
How to remove paralogous alignment from RNAseq data?
RNA-Seq paralogous alignment SNP vcf alignment
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by ★ 1.6k
3
votes
12
replies
3.4k
views
How to call the sample level genotype INFO when certain `FORMAT` fields (or attributes) are missing in some lines of the vcf file?
RNA-Seq software error vcf pyvcf SNP
7.3 years ago by kirannbishwa01 ★ 1.6k
0
votes
2
replies
2.4k
views
PyVCF is giving 'AttributeError' when extracting values from FORMAT and SAMPLE column.
RNA-Seq pyvcf vcf FORMAT GT
7.3 years ago by kirannbishwa01 ★ 1.6k
1
vote
9
replies
4.6k
views
How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf file using pyvcf in python?
vcf python pyvcf FORMAT SAMPLE
7.3 years ago by kirannbishwa01 ★ 1.6k
0
votes
7
replies
2.2k
views
How to do context dependent data merge in python? help ?
python vcf data merge pandas data frame
7.5 years ago by kirannbishwa01 ★ 1.6k
0
votes
1
reply
2.2k
views
How to calculate reference allele frequency in pyvcf and print for all line?
pyvcf vcf python print
updated 7.5 years ago by 43k • written 7.5 years ago by ★ 1.6k
17
votes
8
replies
15k
views
How to select aligned reads below certain mapping Quality (from BWA)?
bwa bam mapping quality alignment samtools
7.6 years ago by kirannbishwa01 ★ 1.6k
3
votes
1
reply
2.6k
views
How to subtract a portion of a bam file from the large bam file of the same sample?
bam alignment samtools merge bedtools
updated 7.6 years ago by 8.6k • written 7.6 years ago by ★ 1.6k
1
vote
3
replies
2.7k
views
Segmentation fault error while running extractPIRs from ShapeIT
ShapeIT segmentation fault error vcf bam
7.6 years ago by kirannbishwa01 ★ 1.6k
1
vote
0
replies
2.5k
views
Can Read Back Phased genotypes be used to extend the haplotype blocks with Beagle, Shapeit, FastPhase etc?
Beagle ShapeIt FastPhase ReadBackPhasing Haplotype
7.6 years ago by kirannbishwa01 ★ 1.6k
0
votes
0
replies
1.7k
views
Are the identified SNPs in the given plot paralogs or positive variants (alleles)?
alignment SNP paralogs alleles
updated 7.7 years ago by 20 • written 7.7 years ago by ★ 1.6k
4
votes
14
replies
11k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality STAR BWA alignment
7.7 years ago by kirannbishwa01 ★ 1.6k
4
votes
3
replies
3.0k
views
How to identify the chromosome where the reads has the secondary (alternative alignments), after running bwa mem?
bwa mem sam bam alignment
updated 7.8 years ago by 14k • written 7.8 years ago by ★ 1.6k
2
votes
2
replies
2.4k
views
Allele specific expression (ASE) using TPM (transcripts per million) values
transcripts per million RNAseq ASE
updated 7.9 years ago by ▴ 260 • written 7.9 years ago by ★ 1.6k
0
votes
0
replies
1.8k
views
Using GEO datasets from NCBI for EHH (extended haplotype homozygosity) test
RNA-Seq ChIP-Seq sequence selection
updated 7.9 years ago by 20 • written 8.1 years ago by ★ 1.6k
3
votes
3
replies
2.8k
views
Haplotype phasing for non-human model organism
phasing impute2 beagle shapeit haplotype
updated 24 months ago by • 0 • written 8.0 years ago by ★ 1.6k
1
vote
4
replies
2.6k
views
VCF isnot compressed and indexed even after running bgzip and tabix,
vcf bgzip tabix compression
8.0 years ago by kirannbishwa01 ★ 1.6k
0
votes
0
replies
2.3k
views
Unable to parse vcf file to create alternate genome and transcriptome database (using g2gtools).
vcf parse g2gtools genome
8.0 years ago by kirannbishwa01 ★ 1.6k
0
votes
6
replies
3.1k
views
Calculate AB (allele balance) using SnpEff/SnpSift
SNPeff SnpSift Allele balance SNP
8.1 years ago by kirannbishwa01 ★ 1.6k
67 results • Page 1 of 2
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