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questions
0
votes
0
replies
337
views
Different colors for different features in IGV
igv
color
7 months ago by
mark.rose
▴ 50
1
vote
1
reply
574
views
bcftools error on freebayes vcfs
vcf
freebayes
bcftools
updated 11 months ago by
Ram
43k • written 2.0 years ago by
mark.rose
▴ 50
0
votes
0
replies
744
views
PacBio's variantCaller's vcf inconsistent with it's consensus sequence
pacbio
variant
variantCaller
vcf
consensus
updated 3.5 years ago by
Biostar
20 • written 3.6 years ago by
mark.rose
▴ 50
1
vote
1
reply
688
views
gatk haplotypecaller report a mush lower coverage than seen in alignment
gatk
alignment
dp
coverage
haplotypecaller
3.6 years ago by
mark.rose
▴ 50
0
votes
2
replies
981
views
VCFs appear inconsistent with view of alignment
vcf
gatk
freebayes
bbmap
igv
3.7 years ago by
mark.rose
▴ 50
0
votes
2
replies
1.1k
views
genome in IGV session file
igv
session
xml
genome
3.8 years ago by
mark.rose
▴ 50
0
votes
5
replies
4.9k
views
freebayes haplotype calling (phased variants)
freebayes
haplotype
phase
phased
variant
updated 4.1 years ago by
mikemc
▴ 10 • written 8.2 years ago by
mark.rose
▴ 50
0
votes
3
replies
872
views
anomalous alignment with bowtie2
bowtie
bowtie2
blast
score
alignment
updated 4.3 years ago by
GenoMax
142k • written 4.3 years ago by
mark.rose
▴ 50
2
votes
13
replies
5.1k
views
unexpected bowtie2 unpaired alignment behavior
alignment
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
mark.rose
▴ 50
0
votes
1
reply
1.8k
views
BBMAP fails to find secondary alignment
bbmap
secondary
updated 5.5 years ago by
Biostar
20 • written 5.6 years ago by
mark.rose
▴ 50
1
vote
6
replies
2.2k
views
BBMAP paired end alignment problem
BBMAP
bbmap
align
paired-end
updated 5.6 years ago by
h.mon
35k • written 5.6 years ago by
mark.rose
▴ 50
2
votes
12
replies
4.3k
views
Picard ExtractIlluminaBarcodes error
picard
extractilluminabarcodes
demultiplex
5.9 years ago by
mark.rose
▴ 50
0
votes
12
replies
1.7k
views
IGV SNP glyph question
igv
SNP
updated 6.1 years ago by
finswimmer
16k • written 6.1 years ago by
mark.rose
▴ 50
0
votes
8
replies
3.8k
views
bbmap paired-end alignment problem
bbmap
align
paired-end
6.2 years ago by
mark.rose
▴ 50
0
votes
2
replies
1.5k
views
jellyfish configure script problem
jellyfish
configure
kraken
6.3 years ago by
mark.rose
▴ 50
1
vote
7
replies
2.0k
views
IGV tracks fail to render even after zooming
igv
track
updated 6.5 years ago by
Jim Robinson
▴ 300 • written 6.5 years ago by
mark.rose
▴ 50
0
votes
5
replies
2.8k
views
calling phased variants
variants
phase
freebayes
platypus
problem
updated 7.1 years ago by
arezansoff
▴ 20 • written 8.1 years ago by
mark.rose
▴ 50
3
votes
2
replies
2.9k
views
INDEL left alignment in bam and vcf
aligner
bowtie
bwa
blasr
indel
updated 7.3 years ago by
Brian Bushnell
20k • written 7.3 years ago by
mark.rose
▴ 50
0
votes
14
replies
3.3k
views
varscan misses alternate variant alleles
variant
insertion
deletion
mpileup
freebayes
7.5 years ago by
mark.rose
▴ 50
0
votes
2
replies
1.4k
views
BG7 usage for bacterial genome annotation
annotation
assembly
updated 11 months ago by
Ram
43k • written 7.5 years ago by
mark.rose
▴ 50
0
votes
1
reply
1.5k
views
BG7 exits prematurely
bg7
annotation
assembly
bacterial
7.5 years ago by
mark.rose
▴ 50
1
vote
5
replies
3.5k
views
Picard MarkDuplicates.jar error
picard
error
duplicates
updated 7.5 years ago by
Dan D
7.4k • written 7.5 years ago by
mark.rose
▴ 50
0
votes
2
replies
2.4k
views
bowtie2 "Pct aligned concordantly >1 times" question
bowtie
bowtie2
concordant
updated 7.5 years ago by
Devon Ryan
104k • written 7.5 years ago by
mark.rose
▴ 50
1
vote
0
replies
1.9k
views
bam-readcount fails to report on all alignments in bam file
bam-readcount
error
warning
alignment
bam
7.5 years ago by
mark.rose
▴ 50
0
votes
3
replies
2.4k
views
bam-readcount fails to report all positions
bam-readcount
bam
variant
alignment
updated 7.8 years ago by
ernfrid
▴ 220 • written 7.8 years ago by
mark.rose
▴ 50
0
votes
0
replies
2.1k
views
Varscan variant calll error on pacbio data
varscan
pacbio
blasr
mpileup
8.0 years ago by
mark.rose
▴ 50
0
votes
2
replies
2.3k
views
bam- readcount error
bam-readcount
bam
updated 8.0 years ago by
ernfrid
▴ 220 • written 8.0 years ago by
mark.rose
▴ 50
0
votes
5
replies
3.5k
views
discordant alignments when bowtie2 set to --no-discordant
software-error
next-gen
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
mark.rose
▴ 50
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