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Showing :
questions
2
votes
6
replies
4.1k
views
Extract heterozygous genotype (GT: 0/1 and 1/2) from the vcf file and calculate allelebalance.
genotype
vcf
heterozygous
allele balance
SNP
8.1 years ago by
kirannbishwa01
★ 1.6k
1
vote
1
reply
2.8k
views
Manipulating header (and contents) of a vcf file
vcf
variants
sed
updated 8.1 years ago by
Ram
43k • written 8.1 years ago by
kirannbishwa01
★ 1.6k
2
votes
3
replies
4.1k
views
How can I best use -c in bwa mem for alignment and to find polymorphisms?
SNP
bwa
mapQ
sequencing
alignment
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
7
votes
8
replies
3.1k
views
Problem running IGB on linux
Integrated-genome-browser
shell
IGB
java
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
0
votes
0
replies
2.0k
views
Genotype matrix to vcf snp database
SNV
vcf
SNP
genotype
variants
matrix
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
5
votes
2
replies
3.5k
views
error while using picard 2.1.0
cleansam
alignment
gatk
picard
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
4
votes
7
replies
3.8k
views
Errors in sam file after bwa SAMPE alignment.
bam
sam
bwa
picard
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
3
votes
5
replies
2.1k
views
Handling/Extracting genome matrix file
snp
allele-frequency
vcf
genome-matrix
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
0
votes
0
replies
2.9k
views
BWA mem vs. Sampe alignment
sequencing
alignment
snp
BWA
8.2 years ago by
kirannbishwa01
★ 1.6k
1
vote
1
reply
2.8k
views
How to account for multiple mapping reads while calling variants?
SNP
BWA
alignment
updated 21 months ago by
Ram
43k • written 8.2 years ago by
kirannbishwa01
★ 1.6k
6
votes
7
replies
3.7k
views
How to remove kmer profiles?
kmers
fastqc
quality filtering
attachments
updated 19 months ago by
Ram
43k • written 8.6 years ago by
kirannbishwa01
★ 1.6k
3
votes
4
replies
5.6k
views
Extracting annotation values from vcf files for plotting distribution
SNP
annotation
updated 23 months ago by
Ram
43k • written 8.3 years ago by
kirannbishwa01
★ 1.6k
0
votes
0
replies
1.4k
views
Details on alignment summary?
adapter_sequence
alignment
bwa
samtools
updated 21 months ago by
Ram
43k • written 8.6 years ago by
kirannbishwa01
★ 1.6k
2
votes
4
replies
5.3k
views
Changing @RG header information in *.bam files using picard
bam
picard
RG-header
sequence
alignment
updated 19 months ago by
Ram
43k • written 8.6 years ago by
kirannbishwa01
★ 1.6k
20
votes
19
replies
5.1k
views
Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations
alignment
RNA-Seq
igb
updated 16 months ago by
Ram
43k • written 8.8 years ago by
kirannbishwa01
★ 1.6k
2
votes
4
replies
2.0k
views
Alignment of genomic resequenced data to reference genome
sequencing
alignment
genome
A.lyrata
Assembly
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
kirannbishwa01
★ 1.6k
0
votes
2
replies
2.0k
views
Quality check for genomic reseq data and aligment to reference genome
sequence
alignment
DNAseq
quality-check
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
kirannbishwa01
★ 1.6k
67 results • Page
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