how to extract all reads covered at the somatic SNP site that from a BAM file in VCF file with using python?

Question

[winter_li]

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 ??

[st.ph.n]

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.