I did an analysis with 3 different BAM file using the Mutectcaller. When I view the VCF file, I didn't see the line starting with "#CHROM POS ID REF ALT QUAL FILTER INFO". There is not any variants in VCF file. What do I need to do to see variants? I share screenshot of VCF file.
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The file viewer only show the first part of the file. You can run ttyd and check the rest of content.
It might be possible for vcf to be empty though. You can guess based on file size or use ttyd to confirm.
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Thank you for your response. I can view variants. Which tool would you recommend I use for variant annotation? I need to find for each variant gene name, type, alteration, protein change, impact, variant allele frequency, reads information.
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The file viewer only show the first part of the file. You can run ttyd and check the rest of content.
It might be possible for vcf to be empty though. You can guess based on file size or use ttyd to confirm.
Thank you for your response. I can view variants. Which tool would you recommend I use for variant annotation? I need to find for each variant gene name, type, alteration, protein change, impact, variant allele frequency, reads information.
Could you post this as a new question to make it easier for community member to search for similar question?
Of course, with pleasure
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