I have used the NA12878 HG001 WES samples 1 - NIST7035 and sample 2 - NIST7086 to run a WES pipeline. I want to confirm if "my-output.vcf" matches to the "Garvan-Output.vcf" file named as follows = project.NIST.hc.snps.indels.vcf.gz output file. (link : https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/)
Could any one suggest as how to check this. Are there known variants which I can check in both outputs to confirm pipeline used.
thank you Smeeta