Question: GATK hg19 bundle question
gravatar for genetic
2.4 years ago by
United States
genetic40 wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.4 years ago by genetic40

copy/pasted from

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 ( mentioned in the same post will be of great help.

ADD REPLYlink modified 2.4 years ago by RamRS25k • written 2.4 years ago by cpad011212k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 685 users visited in the last hour