Generic variation analysis reporting

This workflow generates reports from a list of variants generated by Variant Calling Workflow .

The workflow accepts a single input:

• A collection of VCF files

The workflow produces two outputs (format description below):

1. A list of variants grouped by Sample
2. A list of variants grouped by Variant

Here is example of output by sample . In this table all varinats in all samples are epxlicitrly listed:

Sample POS FILTER REF ALT DP AF AFcaller SB DP4 IMPACT FUNCLASS EFFECT GENE CODON AA TRID min(AF) max(AF) countunique(change) countunique(FUNCLASS) change ERR3485786 11644 PASS A G 97 0.979381 0.907216 0 1,1,49,46 LOW SILENT SYNONYMOUS_CODING D7L tgT/tgC C512 AKG51361.1 0.979381 1 1 1 A>G ERR3485786 11904 PASS T C 102 0.990196 0.95098 0 0,0,51,50 MODERATE MISSENSE NON_SYNONYMOUS_CODING D7L Act/Gct T426A AKG51361.1 0.990196 1 1 1 T>C

Here is an example of output by variant . In this table data is aggregated by variant across all samples in which this variant is present:

POS REF ALT IMPACT FUNCLASS EFFECT GENE CODON AA TRID countunique(Sample) min(AF) max(AF) SAMPLES(above-thresholds) SAMPLES(all) AFs(all) change 11644 A G LOW SILENT SYNONYMOUS_CODING D7L tgT/tgC C512 AKG51361.1 11 0.979381 1 ERR3485786,ERR3485787... ERR3485786,ERR3485787,ERR3485789 ... 0.979381,1.0... A>G 11904 T C MODERATE MISSENSE NON_SYNONYMOUS_CODING D7L Act/Gct T426A AKG51361.1 12 0.990196 1 ERR3485786,ERR3485787... ERR3485786,ERR3485787,ERR3485789... 0.990196,1.0,1.0... T>C

The general idea of the workflow is: