exoseq
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nf-core
Please consider using/contributing to https://github.com/nf-core/sarek
Starting to work on adding proper testcases for ExoSeq now.
In order to get synced with the nf-core template, this repo needs to be prepared accordingly as described in the [nf-core documentation](http://nf-co.re/sync).
GenotypeGVCFs requires > 30 Exomes . We can't test this properly unfortunately, but should aim in providing - a possibility to include more (pre-computed? gvcfs) to run it properly even...
If we support an input mode in which we support sample IDs and multi-lane sequencing configs, it would make sense to split the MultiQC reports into these three tiers: the...
Some sequencing setups will split libraries across lanes. This is currently not modeled in the pipeline. Using a CSV to keep track of IndividualID and sampleID, we could do something...
Picard tools includes comprehensive metrics for exome analysis (target coverage, off target reads etc) - CollectHsMetrics. Include this as a MultiQC input after duplicate marking Example code (report attached): [sample_custom_targets_only.html.zip](https://github.com/nf-core/ExoSeq/files/1950718/sample_custom_targets_only.html.zip)...
For the sake of pulling in relevant meta data, I suggest to use CSV/TSV as default input format rather than a folder with a bunch of FastQ files. Suggested format...
In case we dont have > 30 exomes, we could simply set up the VQSR recalibration step to take 30 exome samples from 1000G and use these as calibration samples....