how to extract all reads covered at the somatic SNP site that from a BAM file in VCF file with using python?
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7.9 years ago
winter_li ▴ 60

HI , I am doing some tumor research. I used GATK to call somatic SNV . now I have the tumor bam file and VCF file . I wanna extract all reads suggested every SNV record from that VCF file . So how to complete that goal with using python ??

alignment next-gen SNP sequencing • 1.6k views
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Do you know python? Or you want someone to throw up a snippet here for you? Did you follow 'GATK Best Practices' to get your VCF? If you know python, you should look more into the format of a VCF file , and then come back with your own attempt to parse these data you've generated.

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