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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:

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Submitting a job in Slurm using wrap

I am trying to create an automatic chain of commands for analyzing biological data. For this I am using Samtools in Slurm cluster. This line below is one of the commands I run for the analysis: samtools view -h file.sam | awk '$6 ~ /N/ || $1 ~…
shaked shanas
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How to install Bioinformatics libraries like trimmomatic, bowtie2, samtools, seqtk etc. in AWS linux OS?

I am not able to find a way to install Bioinformatics and other supported packages in AWS linux based OS while these works in ubuntu and their documentation says they support linux based OS. Is there any command to fix this issue?
optimusPrime
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Piping commands withing GNU parallel (samtools)

I'm trying to run a command in parallel while piping. The reason is that the intermediate files are too big to keep, so I could discard them I have the following codes, that do work separately: #fixmate and convert to bam parallel --verbose --link…
Gabriel G.
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Snakemake Conda environment does not seem to be activating though it says it is

I am running Snakemake with the --use-conda option. Snakemake successfully creates the environment, which should include pysam. I am able to manually activate this created environment, and within it, run my script split_strands.py, which imports the…
ekofman
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Program crashes on VM just when finishing

I am running samtools on a google VM with 8CPUs. It seems that when the process is finished, the program crashes giving the below error. At the same time, there is a problem with the bucket, showing this. Any ideas? Problems with saving the…
user2300940
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applying restriction of files for a loop (for loop) using bowtie2

Hello I just want to apply a loop to a set of files, but instead of doing it to all my files I want to make the loop just only to certain files in a directory Here is the command that I use, is a bowtie2 based alignment of genomic sequences: for i…
Valentin
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Issues with Samtools in OSX Catalina, command line cannot find image of Samtools

I spend a good half a day trying various things to solve the following problem when running samtools running on OSX Catalina: dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from:…
AAA.BioInfo
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How to install ncurses-devel to get samtools to work?

I am on a HPC with no root access and I cannot use the sudo command but I am trying to get samtools-1.10 to work, unfortunately I get the error message: The 'samtools tview' command uses the curses text user interface library. Building samtools with…
genome_juice
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How to split paired-end fastq files?

I have Illumina paired-end reads contained within one .fastq file, denoted as '/1' for forward reads and '/2' for reverse reads. I am using grep to pull out the individual reads and place them into 2 respective files (one for forward reads and one…
Haley
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Remove character from the middle of a string

I have a SAM file with an RX: field containing 12 bases separated in the middle by a - i.e. RX:Z:CTGTGC-TCGTAA I want to remove the hyphen from this field, but I can't simply remove all hyphens from the whole file as the read names contain them,…
lgallagher
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MinGW cannot find my installed zlib.h and zlib files when using mingw32-make to install RSEM

I have looked for hours and cannot seem to find an answer to my issue. I have installed zlib using the sources from zlib.net with mingw32-make -fwin32/Makefile.gcc && mingw32-make install -fwin32/Makefile.gcc like it says in the the Makefile.gcc…
Brian Wiley
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How to decompress/decrypt a single line of a gzip file

The crux here is that this is a huge file. My goal is to avoid reading the entire file into memory at once, AND avoid parsing every line in a loop to get to the line I need (because it takes forever. The file is literally 15 million lines long).…
RightmireM
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package org.scalatest.testng does not exist (intellij)

I'm using IntelliJ IDEA 2017.1.5 on Linux and cannot compile htsjdk with the IDE. Perhaps someone has figured out how? To be clear, htsjdk compiles just fine from the command line, just not in the IDE. To compile, I click on the little recycle icon…
TubesHerder
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Error: Invalid index file: Anaconda

I'm trying to install samtools with conda (Ubuntu 16.04): conda install -c bioconda samtools But i get this index error: Error: Invalid index file: conda-forge/linux-64/repodata.json.bz2 Somebody knows about this? I have tried unsuccessfully to…
fcalles
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How to write rules for software with version specific shell calls? (E.g. Samtools 1.3.1 and 0.1.18)

Thoughts on how to account for a pipeline which can use versions of a software which requires a (slightly) different shell call? At times, switching between versions with conda, the shell calls are different, E.g. Samtools 0.1.18 and Samtools 1.3.1.…
TBoyarski
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