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Tutorial
This section explains how to use main tasks for BiERapp:
The input is a VCF file: individual VCF file for only one sample or multisample VCF file for several samples (families or group of cases /controls). More information about Variant Calling Format.
- After uploading VCF file, BiERapp detects variants for all samples.
- Initial results show the whole set of variants. This is a general first view of detected variants. Next step for each user is defining his own strategy of filtering according to his interests.
There are several filters to define the best strategy of variant selection. It is possible to choose one or several filtering options at the same time:
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Region. Some examples: -Only one chromosomal region: 1:1-10000000
-Several regions (separated by comma): 1:1-10000000, 2:1-10000000
-Some chromosomes: 4,5,8 -
Gene. Only variants for a group of genes. Example: BRCA2,PPL (separated by comma)
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Stats. This filter shows several ways of selecting by allele frequency, genotype frequency, number of mendelian errors, presence of indel, % cases or control for dominant/recessive inheritance. BiERapp also manages efficiently missing values.
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Samples. This intuitive filter that allows reproducing any familiar pedigree with any inheritance model. Also case-control or sporadic de novo mutational diseases can be analysed in this framework. We only have to select the possible genotypes for each sample:
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Control. This filter is based on known population frequencies
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Effect.
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Predicted pathologic effect:
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Consequence types:
- Summary: global statistics and a graphical representation for consequence type.
- Variants and effects: detected variants and its effects for all samples.
- Genome viewer: selected variants can be visualized from this genome browser