Question: How to extract information from a VCF file
0
gravatar for ron
18 months ago by
ron10
Germany
ron10 wrote:

Hi everyone,

I am currently taking an online tutorial on Galaxy and I have managed to complete some of the steps. However, the last one demands working with the final VCF file to determine the amount of SNPs, INDELs, MNVs, etc. I have no idea how to do that. I have already tried a few things googled a little bit, but unfortunately, I haven't got anywhere. I also need to get the names of the genes with the largest number of polymorphic sites.

Any ideas on how to extract this information out of a VCF file? I have even tried with Excel! Although I know that isn't very professional... besides of being quite difficult and impractical to do (not to mention that not even then I have managed to filter this info).

Please any ideas? I will surely give them a try!

Thnx!

snp mnp galaxy indel vcf • 858 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by ron10
4
gravatar for chen.randy
18 months ago by
chen.randy110
chen.randy110 wrote:

use VCF Filter, input such as: -f "TYPE = del" to filter what you need

ADD COMMENTlink written 18 months ago by chen.randy110
0
gravatar for ron
18 months ago by
ron10
Germany
ron10 wrote:

That made it! Thnx! ...and it also helped me to know how to use other filters :-)

ADD COMMENTlink written 18 months ago by ron10
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