Question: 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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gravatar for winter_li
2.7 years ago by
winter_li40
winter_li40 wrote:

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 ??

ADD COMMENTlink written 2.7 years ago by winter_li40

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.

ADD REPLYlink written 2.7 years ago by st.ph.n2.4k
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