Entering edit mode
6.5 years ago
genetic
▴
40
I've downloaded GATK hg19 bundle datasets. Can I use 1000G_phase1.indels.hg19.sites.vcf instead of 1000G_phase1.indels.hg19.vcf? What is difference between these 2 files?
1000G_phase1.indels.hg19.vcf 1000G_phase1.indels.hg19.sites.vcf
Mills_and_1000G_gold_standard.indels.hg19.vcf Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
Thank you in advance. MH
copy/pasted from https://gatkforums.broadinstitute.org/gatk/discussion/1826/indelrealigner-realignertargetcreator-known-site-bundle-files:
FAQs (https://software.broadinstitute.org/gatk/documentation/article.php?id=1247) mentioned in the same post will be of great help.