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Update versions of tools needed (samtools 1.3)
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tseemann committed Jun 7, 2016
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Expand Up @@ -229,14 +229,15 @@ Please submit suggestions and bug reports here: https://github.com/tseemann/snip
* Perl >= 5.6
* BioPerl >= 1.6
* bwa mem >= 0.7.12
* samtools >= 1.1
* samtools >= 1.3
* GNU parallel > 2013xxxx
* freebayes >= 0.9.20
* freebayes sripts (freebayes-parallel, fasta_generate_regions.py)
* vcflib (vcffilter, vcfstreamsort, vcfuniq, vcffirstheader)
* vcflib (vcfstreamsort, vcfuniq, vcffirstheader)
* vcftools (vcf-consensus)
* snpEff >= 4.1

##Bundled binaries
For a modern Linux system (Ubuntu >= 12.04) and Mac OS X all the binaries, JARs and scripts are included.
For Linux (compiled on Centos 5) and Mac OS X all the binaries, JARs and scripts are included.


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