diff --git a/svtyper/classic.py b/svtyper/classic.py index 5b6f580..95f4e18 100755 --- a/svtyper/classic.py +++ b/svtyper/classic.py @@ -433,7 +433,8 @@ def sv_genotype(bam_string, QR = int(split_weight * ref_seq) + int(disc_weight * ref_span) QA = int(split_weight * alt_splitters) + int(disc_weight * alt_span) gt_lplist = bayes_gt(QR, QA, is_dup) - gt_idx = gt_lplist.index(max(gt_lplist)) + best, second_best = sorted([ (i, e) for i, e in enumerate(gt_lplist) ], key=lambda(x): x[1], reverse=True)[0:2] + gt_idx = best[0] # print log probabilities of homref, het, homalt if debug: @@ -468,10 +469,7 @@ def sv_genotype(bam_string, if gt_sum > 0: gt_sum_log = math.log(gt_sum, 10) sample_qual = abs(-10 * (gt_lplist[0] - gt_sum_log)) # phred-scaled probability site is non-reference in this sample - if 1 - (10**gt_lplist[gt_idx] / 10**gt_sum_log) == 0: - phred_gq = 200 - else: - phred_gq = abs(-10 * math.log(1 - (10**gt_lplist[gt_idx] / 10**gt_sum_log), 10)) + phred_gq = min(-10 * (second_best[1] - best[1]), 200) var.genotype(sample.name).set_format('GQ', int(phred_gq)) var.genotype(sample.name).set_format('SQ', sample_qual) var.qual += sample_qual diff --git a/svtyper/singlesample.py b/svtyper/singlesample.py index 0620232..49da119 100644 --- a/svtyper/singlesample.py +++ b/svtyper/singlesample.py @@ -413,7 +413,8 @@ def bayesian_genotype(breakpoint, counts, split_weight, disc_weight, debug): # the actual bayesian calculation and decision gt_lplist = bayes_gt(QR, QA, is_dup) - gt_idx = gt_lplist.index(max(gt_lplist)) + best, second_best = sorted([ (i, e) for i, e in enumerate(gt_lplist) ], key=lambda(x): x[1], reverse=True)[0:2] + gt_idx = best[0] # print log probabilities of homref, het, homalt if debug: @@ -450,10 +451,7 @@ def bayesian_genotype(breakpoint, counts, split_weight, disc_weight, debug): if gt_sum > 0: gt_sum_log = math.log(gt_sum, 10) sample_qual = abs(-10 * (gt_lplist[0] - gt_sum_log)) # phred-scaled probability site is non-reference in this sample - if 1 - (10**gt_lplist[gt_idx] / 10**gt_sum_log) == 0: - phred_gq = 200 - else: - phred_gq = abs(-10 * math.log(1 - (10**gt_lplist[gt_idx] / 10**gt_sum_log), 10)) + phred_gq = min(-10 * (second_best[1] - best[1]), 200) result['formats']['GQ'] = int(phred_gq) result['formats']['SQ'] = sample_qual result['qual'] += sample_qual diff --git a/svtyper/statistics.py b/svtyper/statistics.py index f542e34..51cc3cd 100644 --- a/svtyper/statistics.py +++ b/svtyper/statistics.py @@ -23,7 +23,7 @@ def log_choose(n, k): def bayes_gt(ref, alt, is_dup): # probability of seeing an alt read with true genotype of of hom_ref, het, hom_alt respectively if is_dup: # specialized logic to handle non-destructive events such as duplications - p_alt = [1e-2, 1/3.0, 0.5] + p_alt = [1e-2, 0.2, 1/3.0] else: p_alt = [1e-3, 0.5, 0.9] diff --git a/svtyper/version.py b/svtyper/version.py index 14af72d..6501800 100644 --- a/svtyper/version.py +++ b/svtyper/version.py @@ -1,2 +1,2 @@ __author__ = "Colby Chiang (colbychiang@wustl.edu)" -__version__ = "v0.4.0" +__version__ = "v0.5.0" diff --git a/tests/data/example.gt.vcf b/tests/data/example.gt.vcf index 0c8d68a..4f29b72 100644 --- a/tests/data/example.gt.vcf +++ b/tests/data/example.gt.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.1 -##fileDate=20161212 +##fileDate=20180119 ##reference=/shared/genomes/b37/full/human_g1k_v37.fasta ##INFO= ##INFO= @@ -140,39 +140,39 @@ ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -2 2798774 72354 C 1743.00 . 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