GATK hg19 bundle question

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

gatk

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updated 8.8 years ago by Biostar

• written 8.8 years ago by genetic •

copy/pasted from https://gatkforums.broadinstitute.org/gatk/discussion/1826/indelrealigner-realignertargetcreator-known-site-bundle-files:

the difference between the .vcf and the .sites.vcf files: the .vcf files contain the full callset info including genotypes, while the .sites.vcf files don't contain the genotypes, only the variant sites info. The point of having sites-only files is that they're smaller files

FAQs (https://software.broadinstitute.org/gatk/documentation/article.php?id=1247) mentioned in the same post will be of great help.

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updated 8.8 years ago by Ram

• written 8.8 years ago by cpad0112

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