NGS-Var2017 Exercise.5

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Intersect VCF files using the VCF_intersect module

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From here on, we use data obtained from the full-read set as performance and speed are no issues anymore for the class

The BWA 'mem' algorithms was used to align the NA18507 reads and generated BAM mapping fed to samtools+bcftools and to samtools+varscan to call variants. The resulting variants VCF-files were sorted, compressed, indexed are finally compared here using vcftools.

We will now identify the variant positions shared in both variant lists. The shared variants have more chance to be true than variant in a single caller output because our two callers are using different methods and therefore are biased differently.

• start the VCF_intersect module and link the two VCF placeholders to the full VCF data stored on the server for the bcftools and varscan callers

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Take the files without gatk in the name