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cluster:73 [2020/01/14 14:40]
hmeij07 [Paleogenomics Tools] 		cluster:73 [2020/01/14 14:57]
hmeij07 [Paleogenomics Tools]
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 Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
  
 +  * http://www.htslib.org/download/
   * Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format   * Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
   * BCFtools:Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants   * BCFtools:Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
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 export PATH=/share/apps/CENTOS6/bcftools/1.10.2/bin:$PATH export PATH=/share/apps/CENTOS6/bcftools/1.10.2/bin:$PATH
 export PATH=/share/apps/CENTOS6/htslib/1.10.2/bin:$PATH export PATH=/share/apps/CENTOS6/htslib/1.10.2/bin:$PATH
 +
 +</code>
 +
 +   * https://github.com/ANGSD/angsd
 +   * Program for analysing NGS data
 +
 +<code>
 +
 +# does not seem to work against htslib version above...
 +export  HTSSRC=/share/apps/CENTOS6/ANGSD/htslib
 +export PATH=/share/apps/CENTOS6/ANGSD/angsd:$PATH
  
 </code> </code>
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07

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