akolesnikov
akolesnikov
/ gist:9a4b019e89087dc21cf9ba0b12eece00
Created
December 13, 2018 22:25
Print contig names
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| print('ref_contigs:') | |
| print(','.join('{}:{}'.format(c.name, c.n_bases) for c in ref_contigs)) | |
| print('sam_contigs:') | |
| print(','.join('{}:{}'.format(c.name, c.n_bases) for c in sam_contigs)) | |
| if vcf_contigs: | |
| print('vcf_contigs:') | |
| print(','.join('{}:{}'.format(c.name, c.n_bases) for c in vcf_contigs)) |
akolesnikov
/ hap.py output
Created
December 12, 2018 01:24
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| [I] Total VCF records: 3775119 | |
| [I] Non-reference VCF records: 3775119 | |
| [I] Total VCF records: 126929 | |
| [I] Non-reference VCF records: 95721 | |
| Benchmarking Summary: | |
| Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio | |
| INDEL ALL 10023 9798 225 19035 135 8711 108 0.977552 0.986924 0.457631 0.982215 NaN NaN 1.547658 2.011889 | |
| INDEL PASS 10023 9798 225 19035 135 8711 108 0.977552 0.986924 0.457631 0.982215 NaN NaN 1.547658 2.011889 | |
| SNP ALL 66237 66174 63 77691 53 11426 |