Test-drive the GATK tools and Best Practices pipelines on Terra
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info about small_exac_common_3.vcf.gz
I am using small_exac_common_3.vcf.gz to estimate contamination and I would like to know a few details on what are the filters of that file and what's the source. To be more specific:
1. How many common bi-allelec sites, there are?
2. What's the source of the file?
3. Does it include specific sites? hom, het, all sites from all chr?
4. Does it include extra contigs?
4. are there any filters about AF?
5. Any other filters?
I would appreciate any feedback and guidance.