This repository contains the documentation and results of the CRAVAT variant analysis performed as part of Homework 11 in HIDS-7003. The analysis focused on exploring genomic variants using two VCF files through the CRAVAT platform.

Two VCF files were analyzed:

1. Single-sample VCF file from WES processing: ERR2348724.sorted.indexed.flagged.vcf
2. Multi-sample VCF file from a Thymus Cancer project: 20180912-ThymusSomatic_tumorOnly_wo019_nonres.vcf

• VCF files were downloaded from the CRAVAT homework folder and uploaded to CRAVAT for analysis.
• Each file was processed separately, with settings adjusted to default and reference genome set to hg19.
• Post-analysis, results were explored online using the CRAVAT interface, and relevant outputs were downloaded.

• Aizhan_Uteubayeva-CRAVAT-HW-summary.docx: This document includes a detailed summary of the execution of the pipeline, including screenshots and links to CRAVAT output.

• Gene_Level_Analysis.Result.tsv: Summary of gene-level variant impacts from the CRAVAT analysis.
• Input_Errors.Result.tsv: Details of any input errors detected by CRAVAT during the analysis.
• Variant_Additional_Details.Result.tsv: Provides additional details on variants analyzed in the study.
• Variant_Non-coding.Result.tsv: Analysis results specifically for non-coding regions.
• Variant.Result.tsv: Main results file listing variants and their annotations.

• Similar files as listed for the single-sample analysis, detailing the CRAVAT results for the multi-sample analysis. Each file serves the same purpose, providing comprehensive insights into genomic variants for multiple samples from patients who responded to immuno-therapy.

• Review the Aizhan_Uteubayeva-CRAVAT-HW-summary.docx for a comprehensive understanding of the pipeline execution and output analysis.
• Detailed results and variant analyses can be further explored by accessing the output files listed above.

This project is licensed under the MIT License - see the LICENSE file for details.

• Aizhan Uteubayeva