Questions tagged [samtools]
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
135
questions
1
vote
0
answers
38
views
Mapping statistics from the bam files
I would like to find the mapping statistics from the sorted bam files.
Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
- 11
3
votes
1
answer
24
views
regex: samtools command to "refine" PacBio IsoSeq data?
I am working with preprocessed data (IsoSeq PacBio) and I cannot understand one of the steps:
samtools view -b -e [rq] >= 0.9 flnc.bam
What exactly was ...
2
votes
2
answers
149
views
3
votes
1
answer
97
views
Nextflow Error: failed to read header from "-"
I am trying to run my nextflow pipeline, and have gotten this error:
samtools sort: failed to read header from "-"
I'm not sure why this error is ...
- 65
1
vote
0
answers
35
views
How do I filter reads from a bamfile based on 5' and 3' ends?
I have data in paired-end as well as single-end format for the same sample.I would like to split those two files into two per each, where one contains sequences that have 5' end and the other one has ...
- 11
3
votes
1
answer
61
views
CRISPR genome wide screen analysis using MAGeCK-- Loss of reads/sgRNA using MAGeCK count function?
Sorry if this question seems basic. I am trying to run the MAGeCK pipeline to analyze CRISPR knockout screen data produced by someone in my lab around 5 years ago. I was given the data as bam files ...
4
votes
0
answers
99
views
Write a bash script to run gatk, fix errors with input, and rerun until completion
I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating:
...
- 41
2
votes
0
answers
71
views
Difference between pileup and mpileup in VarScan and samtools
I'm going to call variants with VarScan from a pileup files created with samtools. I realized that there are in general two major possibilities to call variants, pileup as well as mpileup. The VarScan ...
- 153
1
vote
0
answers
64
views
Trinity de novo transcriptome assembly: samtools view failed to add PG line to the header
I have assembled the transcriptome a plant species using Trinity.
Here is the command:
...
- 11
2
votes
1
answer
370
views
how to retain reads with low mapping quality (MAPQ) scores when using samtools view -q
I have been using the -q option of samtools view to filter out reads whose mapping quality (MAPQ) scores are below a given ...
2
votes
1
answer
65
views
Get number of reads with a single, (almost) exact match to the full length of a reference sequence
I can't find an answer to this in previous questions, so hoping someone can help me now.
We have nanopore sequenced a PCR product, and I've filtered our reads to +/- 10 bp of the expected product ...
- 21
1
vote
1
answer
202
views
Different line length in fasta file
I am currently using VEP for variant annotation.
I am facing an error as below:
[E::fai_build_core] Different line length in sequence 'Pn9'
I understand there is ...
3
votes
1
answer
644
views
How to remove the unpaired reads in sam/bam files?
I have sam and bam files for the chimeric reads, which come from two different parts of the genome (For example, the first half of the read from part of Chromosome 1 and the second half of the read ...
- 101
0
votes
1
answer
186
views
Can I use samtools addreplacerg to replace multiple RG entries at the same time?
I have a bam file that contains two @RG lines:
...
- 113
1
vote
2
answers
57
views
Checking that two multiline FASTAs are identical (allowing for different order and lower/upper case)
Is there a good CLI tool that can diff two multiline fasta files, ignoring order, and comparing sequences with identical names with each other pairwise.
Bonus points if lower/upper case is tolerated (...
- 377
0
votes
2
answers
39
views
BAM files with no RNAME and POS, how to map contents to SNPs?
I have a set of 4 .bam files containing the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with ...
2
votes
0
answers
293
views
How to extract reads that map exclusively to a single site with 1 or zero mismatches from BAM files
I generated BAM files (sorted by coordinates) by aligning human RNA reads against the human reference genome using BWA MEM and ...
- 21
3
votes
2
answers
126
views
Detect mutation context in a read of a sam file
After sequencing (Illumina) of some DNA, I generated a sam file through alignment of a fastq file (using Bowtie2). Instead of using variant calling programs, I want to know the specific variances, ...
- 33
1
vote
2
answers
532
views
Potential side effects of replacing read group tags in BAM file
I have a set of BAM files where the read group tags have some (default?) values, i.e.:
@RG ID:RG0 LB:LB0 PU:PU0 SM:SM0
This creates issues in my downstream ...
- 1,773
4
votes
1
answer
280
views
samtools view command not found error
When I tried to use samtools to split a bam file based on different chromosomes, I used this command:
samtools view input.bam -b chr21 | chr21.bam
However, I get ...
- 135
4
votes
1
answer
333
views
BWA mem | samtools view: Intermittent parsing error
Update
The issue was that bwa was running out of memory and failing, but that error wasn't floating to the top (see @Steve's answer, below). I was getting an error ...
- 1,274
2
votes
1
answer
193
views
Samtools sort: most efficient approach to sort a single sample after aligning split .fastq files
Related to my other question (Samtools sort: most efficient memory and thread settings for many samples on a cluster), we need to optimize samtools sort as we ...
- 1,274
2
votes
2
answers
2k
views
Samtools sort: most efficient memory and thread settings for many samples on a cluster
We're preparing to analyze thousands of .bam files beginning with re-alignment, sorting, etc.
Complicated question: Has anyone investigated the optimal thread and ...
- 1,274
0
votes
1
answer
2k
views
How to Sort and Index a SAM file without converting it to BAM?
Generally, I use samtools to sort and index BAM files. Samtools works also with BGZF ...
- 103
3
votes
0
answers
262
views
How to analyze an IGV alignment
I'm working on a project where I am analyzing the performance of an alignment workflow. My goal is to find regions in the resulting BAM file where there are outstanding discrepancies or anything that ...
1
vote
1
answer
54
views
Is there a sam flag for all&none of the reads?
a. Is there a SAM flag that specifies all reads?
b. Is there a SAM flag that specifies none of the reads?
So that if I run samtools view -f (a) -F (b)
the result will be all reads of the file (as if ...
- 177
0
votes
1
answer
148
views
Convert VCF file to mpileup.txt
I am working on an iterative analysis that uses orthologous pipelines that require mpileup.txt files as input for a visualization step. This requires me to convert VCF files to mpileup.txt.
This ...
1
vote
2
answers
367
views
How to extract all sequences mapped to a transcript from Kallisto output
This question has also been asked on Biostars
I ran Kallisto with the --pseudobam option. How do I extract all the short reads that are mapped to a single transcript (e.g. ENST00000367969.8)? As a ...
- 21
1
vote
1
answer
378
views
How to convert multiple single-end bam files to fastq using samtools
Hi I am trying to convert bam files generated from Ion Torrent Proton sequencing to fastq format so that I can upload them to ...
- 41
2
votes
1
answer
44
views
Counting the co-occurrence of variants A and B in an aligned sequencing read
I need some help getting started on this project.
To simplify we want to be able to quantify the occurrence of 3 variants on each sequencing read in an alignment file as a proxy measurement for ...
- 21
0
votes
1
answer
368
views
Is it normal to have a smaller bam file after merging bam files?
I have 2 bam files that belong to the same sample and I merged them with samtools merge. And after merging, I realized that the merged version is a bit smaller than ...
1
vote
2
answers
234
views
Can HTSlib extract bam reads occurring in a specific region without iterating through the whole file?
I am using htslib/sam.h to write a C++ program. As part of this program, I must extract reads occurring on specific scaffolds in specific regions from a bam file. Essentially, I want to perform the ...
- 169
4
votes
4
answers
163
views
Unable to open .bam file in C++ using SeqAn due to 'seqan::UnknownExtensionError'
I am trying to open .bam files in C++ to extract reads occurring at specific scaffolds and loci. I essentially want to call "samtools view sample.bam -o sample.sam scaffold:pos-pos" from C++....
- 169
1
vote
0
answers
512
views
Conversion of SAM to BAM files
I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file .
The command I am using to make very ...
- 143
2
votes
1
answer
43
views
Python package or CLI tool outputting mutations of sequence with respect to reference
I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let'...
- 377
0
votes
0
answers
99
views
seqff script got trouble after samtools treatment
I'm trying to study fetal fraction by using a seqff script from here. The instruction says that I need a headless sam file to work so after alignment with bwa, I process my sam file by using samtools:
...
3
votes
1
answer
894
views
Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
I download a BAM file from ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam (171G), and I am trying to view the comparison result ...
- 31
0
votes
1
answer
153
views
How can I run the latest version of samtools on Slurm?
I am trying to run the following script on slurm to extract information from .sam files. While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. I ...
0
votes
1
answer
246
views
How to perform bowtie2 analysis with slurm?
I am trying to run my alignment script that works locally, using SBATCH.
Official manual for bowtie2 says I can use ...
1
vote
1
answer
1k
views
How can I extract information from .sam files?
I have 10 .sam files after my bowtie2 alignment on ten single-pair sequences. I would like to build a graph based on that output ...
1
vote
1
answer
1k
views
What is "unmapped read segments" in the output of samtools idxstats?
samtools idxstats produces a four column output (see here)
...
- 381
1
vote
1
answer
163
views
How to extract reads with INDELs > a given size?
I'm trying to modify this https://www.biostars.org/p/253774/
To get reads with deletions > 20bp
I think this gives reads with exactly 20bp dels:
...
- 559
2
votes
1
answer
2k
views
How to generate a consensus sequence from a multi-reference BAM file?
I am trying to generate a consensus sequence from a BAM file that was generated by mapping reads to a reference FASTA containing multiple sequences.
Usually, I generate consensus sequences from BAM ...
0
votes
1
answer
248
views
Reading fasta sequence regions with faidx
Im coding in c++ and reading in different reference genomes to examine regions across the chromosomes a few hundred basepairs at a time.
To do it in c++ i use the library htslib and the command ...
- 85
0
votes
1
answer
69
views
How to identify to each scaffold a read belongs to, inside a .sam file?
I have a fasta file assembly and combining it with the raw reads we produced a .bam file which I converted to .sam .
The .sam information lines look like this:
...
- 239
1
vote
2
answers
530
views
Trying to create a .bam file without the need for a .sam file
I'm trying to use the code specified in this link to create a .bam file without the need for a .sam file.
Here is the code I'm using:
...
- 55
1
vote
2
answers
337
views
Mapping statistics from bam file using bbtools and sambamba
Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using reformat.sh from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% ...
- 331
0
votes
0
answers
112
views
summarising read group information from a .bam file
I have merged together 2 different .bam files in order to simulate sample contamination. So the reads can come from one of two samples, as shown by the read group info:
...
- 1,442
0
votes
1
answer
834
views
NO_COOR reads not in a single block at the end 0 -1
I am doing an RNA seq analysis with mouse samples. I had my reads in several lanes, so I concatenated those fastq reads. Then I've mapped my reads with Hisat2 against the new version of mouse "...
- 1
0
votes
2
answers
49
views
Basic question about finding mRNA sequence in transcriptome
I am a computer scientist just starting out in bioinformatics topics, and would appreciate any guidance that can be given here:
I have an mRNA sequence- an isoform - whose length is about 4000 base ...
- 101