map_sample_output_sarek | R Documentation |
See https://nf-co.re/sarek. Most processed outputs are nested by sample and variant callers, i.e.
*VariantCalling/<TUMOR_vs_NORMAL>/<CALLER>
. Other times the data is organized as
*VariantCalling/<CALLER>/<TUMOR_vs_NORMAL>
.
This walks through the output destination (URI of *VariantCalling
)
with similar intention to map_sample_output_rnaseq
, but for Sarek outputs.
map_sample_output_sarek(syn_out, sample_level = 2)
syn_out |
Syn id of syn output destination with files of interest. |
sample_level |
If caller is organized by sample, use 2 (default), if samples organized by caller, use 3. See details. |
Note: And additional step post-Sarek will create MAFs in the output subdirectory DeepVariant. If this is run after the MAF creation step, this will return file indexes with those .maf files.
A data.table
with cols caller
caller_path
caller_syn
output_name
output_id
sample
workflow
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