Genomic analysis

### Program Information

Name: Genomic analysis
Domain: Bioinformatics
Functionality: Analysis of human genomic data – the genomic variant calling pipeline.
Input: The genome of an individual can be sequenced by Next Generation Sequencing (NGS) technology. These reads are stored in a text file called a FASTQ file. This is the input to a variant calling pipeline.
Output: The output of a variant calling pipeline is a text file containing a list of SNV and indels. It is called a Variant Call Format (VCF) file.

#### Reference

A cloud-based framework for applying metamorphic testing to a bioinformatics pipeline https://doi.org/10.1145/2896971.2896975

### MR Information

#### MR1------Deterministic output

Description:
Property: The pipeline is executed independently multiple times with the same FASTQ file. The outputs should be the same.
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#### MR2------Random permutation

Description:
Property: The order of the reads in the FASTQ file is permuted in the follow-up test cases. The outputs of the source and follow-up test cases are expected to be the same.
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Description:
Property: The input reads in the FASTQ file are duplicated in the follow-up input. We expect the output of the follow-up test case include all the variants called in the source output.
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Description:
Property:  Use only the unmapped reads from the source test case as the input to the follow-up test case. We expect no variants would be called in the follow-up test case.
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Description:
Property: Use only the mapped reads from the source test case as the input to the follow-up test case. We expect the outputs of the source and follow-up test cases to be identical.
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