VCF discrepancies

[Cindy Khris Barrios BS]

IGV Version 2.8.13. 

MacOS Catalina Version 10.15.7

MacBook Pro (15-inch, 2018) 

I have two different vcf files containing their corresponding .vcf.gz and vcf.tbi. 

Ex ( 1023_5.g.vcf.gz and 1323_gatk.GRCh.38.vcf)

The output generated from this vcf file (both images below) look different. Both contain ##fileformat=VCFv4.2. I am trying to determine variant calls at a specific gene. The IGV |VCF basics example looks more like 1323-gatk.GRCh38.vcf. My questions are:  How can I determine the discrepancies between the different vcf files.

 

[Cindy Khris Barrios BS]

Sorry, maybe I. was not descriptive enough with my question. I am trying to determine why the variant information track looks different between the different types of vcf files. (In this example, one image is colored "red,blue" and the other one is "grey"). 

Are the discrepancies between the samples due to differences between vcf files or are there settings that I would need to set manually within IGV? Thank you in advance for your support. 

[Helga Thorvaldsdottir]

The variants would be colored grey, for example if they are colored by variant frequency (set in the right-click menu) and the file does not include variant frequency info. You can get info about what's in the file by clicking on the variants, or by looking in the file itself (vcf file format specs can be found here: https://github.com/samtools/hts-specs)

[Cindy Khris Barrios BS]

Thank Helga Thorvaldsdottir, that was very helpful!