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SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014
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00:14, 17 June 2014
Genotype Refinement Output
Remember, type 'q' to quit less.
=== Did I find interesting variants? ===
The region we selected contains ''APOL1'' gene, which is known to play an important role in kidney diseases such as nephrotic syndrome. One of the risk allele, <code>rs73885139</code> located at position <code>22:36661906</code> increases the risk of nephrotic syndrome by >3-folds. Let's see if we found the interesting variant by looking at the VCF file by position.
$GC/bin/tabix $OUT/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 | head -1
Did you see a variant at the position?
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