Computational protocol: Genomic landscape of rat strain and substrain variation

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Protocol publication

[…] For the whole genome sequencing data the 32 strains that were sequenced on Illumina platforms were mapped with BWA mem –M 0.7.5a []. The 10 strains that were sequenced on SOLiD platform were mapped with BWA 0.5.9 aln -c -l 25 -k 2 -n 10 (the latest version to support color space). Picard MarkDuplicates version 1.89 was used to mark all the duplicate reads per rat strain. SNV and indel calling was done following the GATK HaplotypeCaller v2.8-1-g932cd3a best practices from the Broad Institute []. SNVs and indels were annotated using SnpEff version 3.3 h []. Structural variant calling was done using DELLY version 0.3.3 with -q 20 [] and CNVnator version 0.2.7 with a bin size of 1,000 bp []. […]

Pipeline specifications

Software tools BWA, Picard, GATK, SnpEff, DELLY, CNVnator
Application WGS analysis
Organisms Mus musculus, Rattus norvegicus