Created
January 8, 2015 17:46
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Genome STRiP VCF to Plink CNV format
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| #!/bin/env python | |
| import fileinput | |
| idx = 1 | |
| samples = [] | |
| for line in fileinput.input(): | |
| if line.startswith("##"): | |
| continue | |
| if line.startswith("#CHROM"): | |
| samples = line.rstrip().split("\t")[9:] | |
| else: | |
| fields = line.rstrip().split("\t") | |
| chrom = fields[0] | |
| start = fields[1] | |
| end = fields[7].split(";")[0].split("=")[1] | |
| for i in range(len(samples)): | |
| sample_fields = fields[9+i].split(":") | |
| cn = sample_fields[1] | |
| filt = sample_fields[len(sample_fields)-1] | |
| if filt != "LowQual" and cn != "2": | |
| print "\t".join([samples[i], samples[i], chrom, start, end, cn, "0", "0"]) | |
| idx = idx + 1 |
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