Thanks! yes, from the description it should work. I've been trying to install and run vcf tools but haven't managed to do it yet. Can't seem to find a good guide to the vcf install.
I guess there is no simpler way to do this? I've compiled a concatenated file of all my variants that has a sample name column. I am trying to sort by gene name and then pull out all genes that for each gene name, have all sample names...
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It looks like VCFtools' vcf-compare does what you want it to do:
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Filtering over 10 vcf files
Hi there, does anyone know a tool where I can compare more than 2 vcf files at once? I have 10 samples and I want to get common variants among them. I can run Bedtools -IntersectBed 5 times, comparing one to one and that to the other and so on, or try vcf -isec and do the same multistep process. But I'd like to also know if there are subsets within the 10 that I might miss with my method. For example a variant that is common to 7 samples only but not all 10. I couldn't find that by my method as it would depend a lot on the order I do the filtering in.
Any help or suggestions?
Many thanks
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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