- Jul 17, 2018
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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maryamghr authored
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Tobias Marschall authored
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maryamghr authored
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maryamghr authored
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maryamghr authored
subset regions to the regions that have non-zero read count
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Tobias Marschall authored
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- Jul 13, 2018
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maryamghr authored
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Tobias Marschall authored
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- Jul 11, 2018
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daewoooo authored
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Tobias Marschall authored
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- Jul 09, 2018
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Tobias Marschall authored
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- Jul 06, 2018
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Tobias Marschall authored
Added rules to re-genotype a set of given SNVs (e.g. from 1000G) and to do haplotagging of BAM files. Slightly reorganized input file structure: now expect two separate folders "bam/{sample}/selected" and "bam/{sample}/all", where "selected" should contain the good Strand-seq libraries, where all should contain all libraries that can be used for SNV calling/genotyping.
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Tobias Marschall authored
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- Jul 04, 2018
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
Copied script PlottingFunction_SVconsistency/SV_ConsistencyCheck_PlottingFunction.R from strandsequtils repository. Created by Ashley
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Tobias Marschall authored
Update conda environment: this fixes an error "assert_that: assertion must return a logical value", presumably due to a new version of r-assertthat. Also, add scipy (needed for ploidy estimation script) and whatshap (needed for haplotagging).
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Tobias Marschall authored
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Tobias Marschall authored
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Tobias Marschall authored
Re-activate installation of StrandPhaseR in Snakefile. Otherwise the pipeline doesn't work with the bioconda environment. (I hope that this doesn't have side effects on the Singularity workflow.)
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- Jun 27, 2018
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Sascha Meiers authored
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Sascha Meiers authored
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Tobias Marschall authored
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- Jun 26, 2018
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Sascha Meiers authored
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Sascha Meiers authored
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Sascha Meiers authored
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Sascha Meiers authored
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Sascha Meiers authored
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