retrieving fields in vcf file

[Matthew Cserhati]

Hello all,

This isn't exactly pysam, but pyvcf-related. Does anyone know how to retrieve the genotype and the count information from a vcf file using pyvcf? What fields do I have to reference?

So, in this bit of code record.CHROM references the chromosome, POS the position, etc. How do I reference the genotype?

 vcf_reader = vcf.Reader(open(vcffile,'r'))
 for record in vcf_reader:
     s = str(record.CHROM)+" "+str(record.POS)+" "+str(record.REF)+" "+str(record.ALT[0])
     if s in snps:
         print(record)

Thanks, Matthew

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