A list of all the SNPs on a chromosome, including the bases and the depth of coverage from the VCF file

[Szuchieh17]

Ask away!

When I utilized EPI2ME lab to conduct wf-human-variation workflow for SNP calling that generated the VCF file, I cannot obtain information from the IGV viewer integrated with EPI2ME lab, so I directly uploaded the vcf file to the IGV software and obtained some information. Additionally, if I used IGV to perform the profile, I would like to inquire whether it is possible to generate a list of all the SNPs on a chromosome, including the bases and the depth of coverage. This is my situation "What we are looking for is probably from IGV. We hovered the mouse over the colors in the IGV output. A box appeared that gave information on that position. Some had low coverage and an apparent difference between the expected genotype, for instance GT, with what was observed, G. But the coverage was very low. This is what we are looking for across a chromosome." I greatly appreciate your help.

[vlshesketh]

Hi @Szuchieh17, thanks for your interest in the workflow. Would you be able to clarify further what you'd like help with? Is this a case of the workflow not calling variants you are expecting to see, or issues interpreting the output in IGV?

[Szuchieh17]

I knew that wf-human-variation workflow has been integrated with IGV, so I used the latest version to analyze the data again. However, the IGV viewer showed nothing (empty), and I thought that I can directly uploaded to IGV software and view some information as I click the color block like the attached image.

When I show this to my advisor, they asked whether it can be export a list of all the SNPs on each chromosome, including the bases and the depth of coverage. I apologize for any inconvenience. I greatly appreciate your help.