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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 non-synonymous risk allele, <code>rs73885139</code> located at position <code>22:36661906</code> increases the risk of nephrotic syndrome by >2-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?
${GC}/bin/tabix ${OUT}/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 | head -1
22 36661906 . A G 18 PASS DP=409;MQ=59;NS=62;AN=124;AC=2;AF=0.013827;AB=0.4065;AZ=-0.5287;
FIC=-0.0092;SLRT=-0.0075;HWEAF=0.0138;HWDAF=0.0276,0.0000;LBS=36,36,0,0,1,1,0,0;
Let's check the sequence data to confirm that the variant really exists
${GC}/bin/samtools tview $IN{SS}/bams/HG01242.recal.bam $REF{SS}/ref22/human.g1k.v37.chr22.fa
* Type 'g' to go to a specific position

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