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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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Warning in Samtools installation

I recently installed samtools by compiling it using gcc with the command 'make' in linux. Everything went smoothly apart from 2 warnings that appeared: (1) bam_reheader.c:36:19: warning: variable 'old' set but not used…
user3087382
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gcc can't find phtread in cygwin

I'm trying to install samtools () on cygwin. I followed the various tricks here and here but looks like my problem is that i can't have a functioning pthread. gcc is installed and works, zlib is installed and works and ncurses is installed and works…
TriRook
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Running GATK DepthOfCoverage on BAM files with multiple RG's

I am trying to run GATK DepthOfCoverage on some BAM files that I have merged from two original files (the same sample was sequenced on two lanes to maximize the number of reads). I realized after the fact that my merged file has reads with different…
user3245575
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where to copy samtools binary to some directories

I am installing cufflinks on my Mac OS X, and here is the instruction: http://cufflinks.cbcb.umd.edu/tutorial.html Under Installing the SAM tools I follow the instructions below Download the SAM tools Unpack the SAM tools tarball and cd to the SAM…
alittleboy
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Perl: Create index for tab file with two columns

I have got a huge tab-seperated file with up to 200 million rows (normally around 20 million) and two columns: the first column contains an ASCII word with up to 40 chars the second contains an integer. I would like to do the following steps: sort…
Matthias Munz
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Regular Expression - how to capture a number of characters specified in the string

I'm trying to use regular expressions to extract a digit as well as a number of characters equal to that digit from a string. This is for analyzing a pileup summary output from samtools mpileup (see here). I'm doing this is python. As an example,…
CCranney
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My merge overlapping coordinate python script cost too much memory

I'm trying to choose unique regions for my Non-invasive Prenatal Testing (NIPT) project. I have done following steps: Create an artificial fasta file contains 50bp sequence. On each chromosome, the next sequence overlap 40bp from previous…
Rotomegax
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Recommended languages for reading and manipulating BAM and VCF files?

I'm normally a C# / .net developer, but a new project is going to be working with Next Generation Sequencing BAM and VCF files. I will need to read these files, make some changes, and save them. As far as I can tell, there's not much in the way of…
Kyle
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Popen samtools not running

I am writing a function of a class to convert a sam file to bam file, then sort it and index it in python (I know it is easy to fulfill in bash, but it does not hurt to learn more). A sam file has already been generated in the defined directory…
Xp.L
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Java : What is BufferUnderflow Exceptio While using Samtools Java API to get the alienment String with Spcific postion

using Sam-tools Java API how i get seq. between start and end i am write following method it throws Exception . this method write to get Sequences from file . method Goes Here private static List scan(String chromosome, int start, int…
Mohasin Mujawar
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