diff --git a/sufam/__main__.py b/sufam/__main__.py index f17b3ac..5d0ed4a 100644 --- a/sufam/__main__.py +++ b/sufam/__main__.py @@ -202,6 +202,8 @@ def determine_genotype(bp): record.samples = calls if record.FILTER is None: record.FILTER = [] + if record.INFO is None: + record.INFO = {} vcf_writer.write_record(record) @@ -226,6 +228,7 @@ def validate_mutations(vcffile, bams, reffa, chr_reffa, samples, output_format, vcf_reader.formats['GT'] = vcf.parser._Format(id='GT', num=1, type='String', desc="Genotype") vcf_reader.formats['AD'] = vcf.parser._Format(id='AD', num='R', type='Integer', desc="Allelic depth") vcf_reader.formats['DP'] = vcf.parser._Format(id='DP', num=1, type='Integer', desc="Depth") + vcf_reader.column_headers = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT'] vcf_writer = vcf.Writer(outfile, vcf_reader) else: vcf_reader = open(vcffile)