alviitayyaba / single-nucleotide-variants-hands-on

Single nucleotide variants hands-on

Task completion using SNPEff and SNPSift tools:

1.) Discard all the variants which are failed to pass the filtering

A) Through attached R code

B) Through SNPSift

cat tasks/task3/tumor_vs_normal.strelka.somatic.snvs.vcf | java -jar $SNPSift filter (“FILTER==’PASS’)” > filtered.vcf

2.) Annotate filtered variants with the SNPeff using hg19 database

java -jar $SNPEff hg19 tasks/task3/filtered.vcf > tumor_vs_normal.strelka.somatic.snvs.ann.vcf

3.) Count the variants that change the protein encoded by the gene in which the variant is located. The list of possible consequences of changes

java -jar $SNPSift filter "ANN[*].EFFECT has 'missense_variant'" tasks/task3/tumor_vs_normal.strelka.somatic.snvs.anno.vcf > filter_missense_any.vcf

4.) List a genes which are affected with the predicted Loss of function effect.

cat tasks/task3/tumor_vs_normal.strelka.somatic.snvs.anno.vcf | java -jar $SNPSift filter "(exists LOF[].PERC) & (LOF[].PERC > 0.5)" > tasks/task3/filtered-LOF.vcf

Supplimentary data:

tumor_vs_normal.strelka.somatic.snvs.vcf.gz