Monthly Archives: May 2015

SAMtools, BCFtools and HTSlib 1.2

General Information

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

Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
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.


How to use It

They are installed in /software/samtools-1.2//software/bcftools-1.2/ and  /software/htslib-1.2.1 respectibely.

Something like this should be added in the PBS script.

export PATH=/software/samtools-1.2/bin:/software/bcftools-1.2/bin:$PATH

export LD_LIBRARY_PATH=/software/htslib-1.2.1/lib:$LD_LIBRARY_PATH


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