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10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
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Generating VCF File #49

Closed sahh04 closed 3 years ago

sahh04 commented 3 years ago

Hi,

I am a high school student working on a single cell seq project and I was wondering what tools would be required to generate a VCF file, as I haven't been able to find much information anywhere?

Thanks

pmarks commented 3 years ago

Hi @sahh04, you can use Freebayes or GATK to generate VCFs from a BAM file. You should read up on the general topic of 'variant calling' for next generation sequencing (NGS), then things will make more sense.