Hi,
I'm biology student doing my masters thesis in NGS. I have whole exome data from FIMM and have been filtering it. I have a excel table with the SNP's and .bam files for visualizing.
The case is a rare cartilage syndrome (only one patient) and I have exome data from the one patient, his mom, and three controls. I have filtered the patients exome data using the other datas, and restricted the SNP's to ones not found in public databases. To further narrow the search down, I also dis-included ones not located in known genes... Now I still have ~400 SNP's left. I already manually picked out and looked at SNP's in genes I know to be important in cartilage (collagens etc.). However, I would like to continue the analysis with rest of the 400 SNP's...
I would like to do some functional annotation, so that i could only look at the non synonymous mutations. How can I do this when I don't have vcf-files?
I'm biology student doing my masters thesis in NGS. I have whole exome data from FIMM and have been filtering it. I have a excel table with the SNP's and .bam files for visualizing.
The case is a rare cartilage syndrome (only one patient) and I have exome data from the one patient, his mom, and three controls. I have filtered the patients exome data using the other datas, and restricted the SNP's to ones not found in public databases. To further narrow the search down, I also dis-included ones not located in known genes... Now I still have ~400 SNP's left. I already manually picked out and looked at SNP's in genes I know to be important in cartilage (collagens etc.). However, I would like to continue the analysis with rest of the 400 SNP's...
I would like to do some functional annotation, so that i could only look at the non synonymous mutations. How can I do this when I don't have vcf-files?
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