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1,233 results • Page
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SAMTOOLS
•
reset
199
Votes
24
Replies
139k
Views
16 follow
How To Filter Mapped Reads With Samtools
samtools
8.2 years ago
sohadb1357
• 500
• updated 19 months ago
ibseq12
• 0
0
Votes
4
Replies
284
Views
samtools fixmate: Couldn't write to output file: Broken pipe
alignment
samtools
bwa
sed
21 months ago
Ric
• 240
• updated 19 months ago
Biostar
20
9
Votes
8
Replies
245
Views
Divergent number of replicates between FastQC and samtools
fastqc
STAR
samtools
20 months ago
user31888
• 60
• updated 20 months ago
i.sudbery
4.7k
5
Votes
5
Replies
199
Views
How to parse BAM files without requiring huge memory?
software error
sequence
samtools
20 months ago
kimon.frousios
• 20
2
Votes
4
Replies
163
Views
Extract target region sequence with samtools but the output contains suquence exceeding the bed region
bed
samtools
20 months ago
xusijiamed
• 0
• updated 20 months ago
i.sudbery
4.7k
0
Votes
1
Reply
160
Views
CIGAR inconsistency BWA/GATK
bwa
samtools
genome
sequence
alignment
20 months ago
ncoca
• 0
5
Votes
10
Replies
181
Views
.sra to bam conversion results in a "< myfile > does not have BAM or CRAM format error"
SRA-toolkit
samtools
deeptools
20 months ago
jordi.planells
• 70
• updated 20 months ago
genomax
68k
0
Votes
1
Reply
190
Views
Merging BAM file with Samtools
samtools
merge
BAM
20 months ago
seta
♦ 1.2k
• updated 20 months ago
Devon Ryan
90k
24
Votes
6
Replies
49k
Views
7 follow
Merging Bam Files
picard
samtools
9.0 years ago
Tryingtogetthere
• 170
• updated 20 months ago
abhijit.synl
• 50
0
Votes
0
Replies
103
Views
Samtools mpileup with 10x data
mpileup
samtools
20 months ago
lali1
• 0
3
Votes
1
Reply
131
Views
Unexpected characters at consensus fasta generated by mpileup
samtools
mpileup
consensussequence
20 months ago
gokberk
• 30
4
Votes
14
Replies
245
Views
How to sort sam file using shell script?
samtools
sort
sam file
Forum
20 months ago
gerrybio2010
• 0
• updated 20 months ago
Bastien Hervé
4.2k
5
Votes
5
Replies
1.9k
Views
samtools flagstat result is different from samtools view result
SAMtools
4.9 years ago
Louis Kok
• 10
• updated 20 months ago
macielrodriguez2
• 10
3
Votes
2
Replies
131
Views
report every base in a bam using bed as input
samtools
bcftools
20 months ago
bioguy24
• 190
• updated 20 months ago
Pierre Lindenbaum
120k
0
Votes
5
Replies
168
Views
MarkDuplicates: Mates are missing
rna-seq
trimmomatic
Hisat2
picardtools
samtools
20 months ago
swarajgaikwad15
• 0
3
Votes
8
Replies
502
Views
7 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
23 months ago
chparada
• 0
• updated 20 months ago
guillaume.rbt
• 590
1
Vote
3
Replies
135
Views
How can bam file only retain potential variants?
bwa
sam
samtools
20 months ago
gerrybio2010
• 0
0
Votes
3
Replies
1.7k
Views
How to generate vcf using samtools Version: 0.1.19-96b5f2294a?
samtools
vcf
ubuntu
21 months ago
Vijay Lakhujani
4.1k
5
Votes
4
Replies
234
Views
HISAT2 output direct to bam
RNA-Seq
samtools
21 months ago
Adrian Pelin
♦ 2.3k
• updated 21 months ago
ATpoint
17k
3
Votes
5
Replies
210
Views
Loss of reads during realignment bam
gatk
bwa
wgs
fastQValidator
samtools
21 months ago
mb2subi
• 0
0
Votes
1
Reply
170
Views
Calling haploid consensus sequence from vcf
vcf
samtools
bcftools
consensus
haploid
21 months ago
philodendron
• 0
• updated 21 months ago
Kevin Blighe
43k
5
Votes
3
Replies
5.1k
Views
Problems When Calling Snps Using Samtools Mpileup
samtools
snp
calling
8.2 years ago
玄
• 20
• updated 21 months ago
Biostar
20
0
Votes
1
Reply
154
Views
Samtools mpileup - Sudden decrease of coverage at homopolymer regions
samtools
mapping
mpileup
21 months ago
Louis Kok
• 10
• updated 21 months ago
Kevin Blighe
43k
1
Vote
5
Replies
332
Views
SNP calling with SAMtools on multiple samples
SNP
samtools
vcf
bam
22 months ago
madeira.ag
• 0
• updated 21 months ago
Begali
• 0
1
Vote
7
Replies
266
Views
mpileup format to vcf
next-gen
snp
samtools
21 months ago
AGE
• 20
12
Votes
7
Replies
2.8k
Views
Trying To Pull Regions From An Online Bam File Without Downloading
samtools
igv
bam
8.6 years ago
Wjeck
• 480
• updated 21 months ago
Biostar
20
0
Votes
3
Replies
241
Views
count reads mapped to multiple locations only once
bwa
alignment
samtools
multiple mapping
21 months ago
snishtala03
• 10
1
Vote
1
Reply
257
Views
samtools stats result different from samtools flagstat
samtools
21 months ago
snishtala03
• 10
0
Votes
2
Replies
174
Views
samtools sort: truncated file. Aborting
samtools
alignment
picard
21 months ago
m.t.lorenc
• 0
0
Votes
3
Replies
179
Views
bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the single .bam file?
alignment
sort
bowtie2
samtools
21 months ago
dongchenchen
• 10
• updated 21 months ago
h.mon
25k
9
Votes
7
Replies
282
Views
Samtools segmentation fault when extracting exons from bam file.
rna-seq
alignment
seg fault
samtools
22 months ago
jstevenson2256
• 10
• updated 22 months ago
Damian Kao
15k
0
Votes
3
Replies
194
Views
How to find all the region where one read is mapped in a bam file
NGS
SAMTOOLS
DNA
Mapping
sequencing
22 months ago
prasoongama
• 0
• updated 22 months ago
WouterDeCoster
39k
0
Votes
2
Replies
283
Views
bcftools / samtools, which database does the MAF function use?
bcftools
samtools
MAF
22 months ago
Davide Chicco
• 80
• updated 22 months ago
Pierre Lindenbaum
120k
1
Vote
4
Replies
273
Views
Filtering BAM file to include PE reads that did not map, even though their mate did
BAM
samtools
filter
mapping
read
22 months ago
nute11a
• 0
• updated 22 months ago
Istvan Albert
87k
0
Votes
0
Replies
130
Views
Variant Calling between Microbial Populations
Variant
snp calling
populations
samtools
22 months ago
gabriel.jabud
• 0
0
Votes
2
Replies
218
Views
How to get output with read counts and read count percentages from bam file?
read counts
bam
samtools
picard
22 months ago
bayramliaziz
• 0
• updated 22 months ago
WouterDeCoster
39k
7
Votes
19
Replies
919
Views
Error with samtools rmdup
ChIP-Seq
samtools
2.8 years ago
Bella_p
• 50
• updated 22 months ago
Biostar
20
0
Votes
7
Replies
211
Views
Bcftools Call method not detecting single nucleotide deletions?
bcftools
samtools
variant
variant calling
22 months ago
kennyworkman
• 0
1
Vote
1
Reply
160
Views
Replace @RG group by the one of another BAM
samtools
addreplacerg
22 months ago
da.de
• 0
• updated 22 months ago
RamRS
21k
0
Votes
1
Reply
176
Views
How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
SNP
hESC
WES
samtools
22 months ago
maria2019
• 30
3
Votes
5
Replies
269
Views
How to find a variant in a particular position in a bam file only using samtools
bam
sam
samtools
22 months ago
tw617
• 30
• updated 22 months ago
swbarnes2
5.7k
3
Votes
11
Replies
357
Views
How to calculate percent identity from sam file?
mapping
assembly
sam
samtools
cigar
22 months ago
O.rka
• 110
0
Votes
3
Replies
212
Views
Get read start site using bedtools from bam file after merging paired end data
RNA-Seq
bbmerge
bedtools
samtools
alignment
22 months ago
snishtala03
• 10
2
Votes
1
Reply
216
Views
Mauve alignment vs samtools for SNP calling
samtools
SNP
mauve
alignment
snp calling
22 months ago
gabriel.jabud
• 0
• updated 22 months ago
Joe
12k
1
Vote
1
Reply
228
Views
How do get additional bam statistics
RNA-Seq
alignment
bam
samtools
22 months ago
t-jim
• 30
4
Votes
8
Replies
238
Views
Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: stdout=, stderr=samtools view: invalid option -- ' ''
pysam
samtools
22 months ago
SDin
• 0
• updated 22 months ago
ATpoint
17k
1
Vote
2
Replies
2.7k
Views
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
software error
snp
genome
samtools
bcftools
4.9 years ago
david.4.ray
• 10
• updated 23 months ago
zx8754
7.5k
3
Votes
2
Replies
164
Views
Sorting of bam files
RNA-Seq
samtools
23 months ago
Liftedkris
• 10
• updated 23 months ago
ATpoint
17k
4
Votes
5
Replies
278
Views
Question: Is samtools BAQ redundant after GATK's IndelRealinger
samtools
indels
23 months ago
James Reeve
• 80
4
Votes
4
Replies
246
Views
How to remove bam files that don't contain matching reads
bowtie2
samtools
BAM
23 months ago
samlambrechts299
• 130
• updated 23 months ago
Pierre Lindenbaum
120k
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