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Showing top results for tag:
samtools
•
reset
0
votes
0
replies
45
views
samtools depth and sambamba depth produce different results
sambamba
samtools
depth
coverage
1 day ago by
Johannes
• 0
1
vote
3
replies
154
views
BWA mem or samtools have any parameter to filter the mismatch reads?
mapping
samtools
reads
BWA
1 day ago by
Damon_Wan
• 0
2
votes
2
replies
87
views
Samtools view filter by reference sequence
samtools
2 days ago by
maxrwjones898
• 0
2
votes
3
replies
164
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin
samtools
bcftools
vcf
split-vep
updated 3 days ago by
David Parry
▴ 60 • written 4 days ago by
dare_devil
★ 1.4k
0
votes
0
replies
52
views
Samtools vcf file filtering
samtools
RNAseq
sequencing
7 days ago by
bandanaschapagain
▴ 30
2
votes
7
replies
372
views
Coverage NGS reads
NGS
samtools
coverage
7 days ago by
Sabeen
• 0
4
votes
4
replies
221
views
Samtools sort: too many open files error
samtools
sort
updated 7 days ago by
jkbonfield
▴ 510 • written 4 weeks ago by
rekren
▴ 30
0
votes
3
replies
205
views
How to extract consensus sequence for a genomic region from a bam file
samtools
bam
9 days ago by
michael.flower.14
• 0
2
votes
4
replies
201
views
ATAC-seq - remove mt reads using KMC
samtools
chrM
ATAC-seq
mitochondria
KMC
12 days ago by
maxrwjones898
• 0
0
votes
0
replies
69
views
error that occurred when I ran velocyto on bam files
bamfiles
velocyto
samtools
updated 17 days ago by
rpolicastro
5.1k • written 17 days ago by
gabriella.wangyi1986
• 0
2
votes
4
replies
321
views
samtools multithreads
samtools
14 days ago by
Palgrave
▴ 30
0
votes
1
reply
171
views
What does the -0 flag of samtools fastq mean?
samtools
updated 20 days ago by
aw7
▴ 10 • written 20 days ago by
O.rka
▴ 290
6
votes
6
replies
1.9k
views
6 follow
Issue With CRAM -> BAM -> FASTQ Conversion
samtools
fastq
cram
bam
view
updated 21 days ago by
bw.
▴ 160 • written 21 months ago by
denis.k
▴ 20
0
votes
2
replies
180
views
How can a duplicate read be interchromosomal?
interchromosomal
duplicate
NGS
samtools
picard
23 days ago by
maxrwjones898
• 0
2
votes
2
replies
103
views
Can't create tabix index of the bed file
samtools
tabix
bed
ATAC-seq
updated 29 days ago by
desouzareis.r
▴ 220 • written 29 days ago by
i.am.filippov
• 0
3
votes
3
replies
118
views
Samtools sort by name - bam size issue
alignment
genome
samtools
updated 5 weeks ago by
Pierre Lindenbaum
135k • written 5 weeks ago by
quentin54520
• 0
1
vote
2
replies
102
views
Getting reference sequence for set of reads
RNA-Seq
alignment
samtools
bedtools
updated 5 weeks ago by
Biostar
20 • written 6 weeks ago by
martin.grasshoff
• 0
1
vote
15
replies
294
views
Picard ValidateSamFile Error: "ValidateSamFile Value was put into PairInfoMap more than once"
samtools
bam
sam
picard
alignment
15 days ago by
stephen.johnson.online
• 0
0
votes
3
replies
141
views
Bam files not accepted in dba.count
samtools
diffbind
dba.count
bam
5 weeks ago by
corinne_hutfilz
• 0
0
votes
0
replies
113
views
Total number of trimmed reads less than number of mapped reads
alignment
next-gen
sequence
SAMtools
BWA
6 weeks ago by
kspata
▴ 70
0
votes
0
replies
154
views
Bowtie2 Alignment Summary vs Samtools
alignment
bowtie2
samtools
6 weeks ago by
Ar
★ 1.1k
0
votes
3
replies
113
views
strange looking bcftools norm file
bcftools
bcftools norm
samtools
variant
6 weeks ago by
amy_houseman
▴ 20
1
vote
5
replies
124
views
Problems removing specific contig from .bam file
genome
picard
samtools
.bam
WGS
updated 6 weeks ago by
Pierre Lindenbaum
135k • written 6 weeks ago by
USA_225478
• 0
1
vote
1
reply
2.2k
views
Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings
samtools
mpileup
bam
ngs
updated 7 weeks ago by
aroob.lab
• 0 • written 8.0 years ago by
tsk
▴ 10
0
votes
6
replies
119
views
Estimate edit distance to a reference for a subset of bases in reads (bam files)
next-gen
bam
samtools
sequence
updated 8 weeks ago by
Pierre Lindenbaum
135k • written 8 weeks ago by
AQ7
▴ 30
3
votes
3
replies
234
views
How to plot alignment statistics; how many reads are mapped to the genome?
samtools
RNA-Seq
8 weeks ago by
anamaria
▴ 160
2
votes
3
replies
169
views
Convert processed bam file to fastq
alignment
sequence
bam
samtools
fastq
updated 9 weeks ago by
GenoMax
99k • written 9 weeks ago by
coltonrobbins73
• 0
5
votes
4
replies
158
views
Converting CRAM to BAM without reference fasta
samtools
BAM
CRAM
9 weeks ago by
Ld_60
▴ 40
0
votes
0
replies
128
views
missing informations in VCF file (read mapping)
vcf
mapping
samtools
bcftools
updated 9 weeks ago by
Pierre Lindenbaum
135k • written 9 weeks ago by
romain.derelle
• 0
1
vote
1
reply
112
views
bwa mem piped to samtools is not working strange error
samtools
bwa mem
9 weeks ago by
Dataminer
★ 2.7k
1
vote
3
replies
177
views
Compare Differences in a sequence between a SAM file and a FASTA file
genome
python
samtools
10 weeks ago by
lozfromcorby
• 0
0
votes
1
reply
1.2k
views
interpolation y vector
sequencing
matlab
samtools
bam
updated 10 weeks ago by
Biostar
20 • written 6.2 years ago by
mosquitoes
• 0
0
votes
11
replies
223
views
Error when trying to convert BAM file to FASTQ.
samtools
bedtools
10 weeks ago by
DNAngel
▴ 120
0
votes
4
replies
2.2k
views
Mapping shorts reads using Bowtie
bowtie
mapping
index
samtools
updated 10 weeks ago by
Biostar
20 • written 5.8 years ago by
bioinfo
▴ 790
1
vote
1
reply
135
views
Sorting BAM files never fully finished
readmapping
samtools
Tool
updated 10 weeks ago by
ATpoint
48k • written 10 weeks ago by
dolphin6906
• 0
0
votes
1
reply
150
views
How to sort a FASTA file and (its) BAM file in the same order?
fasta
bam
samtools
11 weeks ago by
Dunois
▴ 620
1
vote
3
replies
163
views
How to get samtools flagstats results from samtools view
samtools
flagstat
11 weeks ago by
alexandriapinto1
• 0
0
votes
5
replies
213
views
add sample name to bam header based on bam file name
samtools
updated 12 weeks ago by
Pierre Lindenbaum
135k • written 12 weeks ago by
Ana
▴ 180
3
votes
6
replies
156
views
Extract the overlapping paired-end reads
samtools
paired-end reads
12 weeks ago by
Ar
★ 1.1k
9
votes
1
reply
146
views
Calling triovariants using varscan from a compressed mileup file ?
varscan
samtools
trio
mpileup
pipe
updated 12 weeks ago by
svp
▴ 420 • written 3 months ago by
dare_devil
★ 1.4k
0
votes
0
replies
157
views
convert bam to cram with non-local reference fasta
samtools
cram
12 weeks ago by
Ana
▴ 180
10
votes
4
replies
177
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
3 months ago by
dare_devil
★ 1.4k
3
votes
3
replies
4.5k
views
error with vcfutils when building consensus sequence with samtools and bcftools 1.2
samtools
vcfutils
consensus sequence
mpileup
updated 3 months ago by
aebrahimi58
• 0 • written 6.2 years ago by
cheng
▴ 20
1
vote
3
replies
165
views
Combine multiple samtools view
samtools
bam
alignment
updated 3 months ago by
GenoMax
99k • written 3 months ago by
rah
▴ 20
0
votes
1
reply
192
views
samtools idxstats showing accession number and genomic scaffold
samtools
idxstats
bams
updated 3 months ago by
Pierre Lindenbaum
135k • written 3 months ago by
whb
▴ 20
0
votes
3
replies
365
views
bcftools missing most indels in variant calling
Assembly
samtools
bcftools
updated 3 months ago by
finswimmer
14k • written 3 months ago by
esinpublic-2012
• 0
2
votes
6
replies
626
views
How do I make a fasta reference file from a set of bam files in order to maximize the number of heterozygotes in my reference genome?
samtools
mpileup
bcftools
vcfutils
seqtk
updated 3 months ago by
Biostar
20 • written 4 months ago by
fabiopertille
• 0
0
votes
0
replies
205
views
Multisample BAM file
bam
snp calling
samtools
written 3 months ago by
gubrins
▴ 70
2
votes
3
replies
229
views
Modify query names longer than 252
samtools
fastq
awk
minimap2
updated 3 months ago by
5heikki
9.7k • written 3 months ago by
leonardo.caserta
• 0
0
votes
6
replies
282
views
Trying to understand samtools -f and -F
samtools
bowtie2
alignments
mapping
3 months ago by
shibl_a
▴ 20
50 results • Page
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Recent Votes
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Comment: Hunting invisible characters?
Comment: Hunting invisible characters?
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Thank you so much for informing me. I've removed the reference numbers in the body of the article, and I find the platform seems to be unab…
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Thank you, using `dos2unix` worked perfectly!
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Please do not delete posts that have comments/answers.
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