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Showing : 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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