Filtering SVTyped lumpy

gistfile1.txt

from cyvcf2 import VCF
import numpy as np

my_vcf = VCF('-')

#print my_vcf.raw_header,
samples = np.array(my_vcf.samples)

for variant in my_vcf:
    gts =  variant.gt_types

    non_ref = samples[(gts != 0) & (gts != 2)]

    if ((1 in variant.gt_types) or (3 in variant.gt_types)) \
            and (2 not in variant.gt_types) \
            and variant.QUAL > 100 \
            and np.median(variant.format('GQ', float)) > 100:
        #print str(variant),

        print variant.CHROM + "\t" + variant.ID +"\t" + str(variant.QUAL) + "\t" +  str(variant.INFO['SU']) + "\t" + str(variant.format('AO', int).max()) + "\t" + str(len(non_ref)) + "\t" + "\t".join(non_ref)