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Questions tagged [samtools]

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

  1. Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
  2. Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
  3. HTSlib A C library for reading/writing high-throughput sequencing data Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Links:

115 questions
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BWA can't find the local index file

I'm currently trying to import a .fasta file into bwa to use a reference genome to map my reads to. However, i currently am getting this error: [E::bwa_idx_load_from_disk] fail to locate the index files Any help? Here is my code:…
Haley
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Detect large deletions from CIGAR string

I am new to sequence analysis and I'm doing some exercises to help me learn to use pysam and samtools for WGS data analysis. One thing I would like to do is to detect (rather large) deletions from 2D Oxford nanopore data (large reads). For this…
Sigurgeir
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An issue about pysam installation

It's linux, using conda to install pysam, and pip install pysam keep failing. After successful installed pysam, pysam shows in conda list and appears in anaconda2/pkgs/ but when import pysam in python 2.7.12, it failed by Traceback (most recent…
Lucas Lau
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Is there a way to save an entire "alignment field/column" into a NumPy array using Samtools?

In the SAM format, each alignment line represents the linear alignment of a segment, and each line have 11 mandatory fields, i.e. QNAME, FLAG, RNAME, POS, MAPQ, etc. Let's say I wanted a NumPy array of all "QNAMES" in a given BAM file. Or, one…
ShanZhengYang
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How to use htslib/samtools to transform SAM/BAM reads?

I'm using the htslib library for reading SAM/BAM files, it works perfectly. I can also write the alignments back to a new SAM/BAM file. For example, the following code prints the DNA sequence of an alignment: bam1_t *b = ...; int i; for…
ABCD
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How to use pysam.view to emulate all functions of samtools view

I am trying to use pysam.view() to filter out certain alignments from a BAM file. The problem I am facing is how to include several regions in the filter. pysam.view() emulates the samtools view command which allows one to enter several regions…
Chaus
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Error using DEXSeqDataSetFromHTSeq

Currently I am trying to understand DEXSeq package. I have a design tsv file and 7 files which contains Counts. Now would like to run the following command library("DEXSeq"); design=read.table("dexseq_design.tsv", header=TRUE, row.names=1); ecs =…
Jumaa Khan
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How to compile and work samtools with cygwin

I need some help to resolve this problem. I got an error when I compiled Samtools under Cygwin (windows 8 64 bit). I got the following message: ADMIN@USER ~/samtools-0.1.19 $ make make[1]: Entering directory…
user3455175
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Multi-BAM visualization with Tablet alignment viewer

I have been using the Tablet alignment viewer (http://bioinf.scri.ac.uk/tablet/) to visualize my bam alignment files. Because I want to compare different individuals, I need to open 2 or 3 BAM together on the same window. But Tablet doesn't seem to…
kostas_bcn
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How to install tophat in Debian?

I have tried searching and trying everything. I have bowtie, samtools and libbam-dev installed in my system. While running ./configure I am getting this error: checking for bamlib... configure: error: We could not detect the bam libraries (version …
New Folder
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works on the command line but not in a shell script

I have this line samtools view -h file | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o output the dash between the -S and the -b is supposed to indicate to the program that it is from STDIN. I can run it from a perl script on the command…
user1234579
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How to run a command on multiple files within subdirectories with similar file suffix?

I am still battling to understand and improve my command line skills. This time, I have a directory with 25 subdirectories. In each subdirectory, there are 4 sorted bam files which I want to index. I do not want to go to each subdirectory and…
user20330606
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Extracting ITS Region from Paired-end FASTQ Data Using a Reference Genome: Guidance Needed

I have 20 isolates labeled as A_1 to A_50. For each isolate, I have paired-end FASTQ files. I also have a reference genome file available. I would like to extract the sequences of ITS (Internal Transcribed Spacer) region from each isolate using the…
kolom
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Pysam view yield reads one at a time

I'm trying to using pysam to filter a .bam file for mapping quality and excluding flags. I know I can use .fetch() and iterate through reads that way, but I'm guessing it's faster to first use pysam.view() However, when I try this on a large .bam,…
rbierman
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Problem with viewing bam file downloaded from geo

I downloaded a dataset in the BAM Format from GEO using the command: prefetch SRR13558458 It generates a file names "SRR13558458.sra". I would like to view this file using samtools. But it seems this sra file which is a bam file is not readable…
Mahgen
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