Changes

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.

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  

  ${GC}/bin/tabix ${OUT}/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 | head -1  

Did you see a variant at the position?

Did you see a variant at the position?

  $GC/bin/tabix $OUT/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 | head -1  

  ${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;

  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;

                     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

Let's check the sequence data to confirm that the variant really exists

  $GC/bin/samtools tview $IN/bams/HG01242.recal.bam $REF/human.g1k.v37.chr22.fa

  ${GC}/bin/samtools tview ${SS}/bams/HG01242.recal.bam ${SS}/ref22/human.g1k.v37.chr22.fa

* Type 'g' to go to a specific position

* Type 'g' to go to a specific position