From 32349bb43028d0928493f98c876e5be11b1a2e92 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Mon, 27 Jan 2020 14:45:38 +0100
Subject: [PATCH] added filter_monomorph and filter_callrate flag added
---
svreader/annotation.py | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/svreader/annotation.py b/svreader/annotation.py
index af72a34..51ac2d1 100644
--- a/svreader/annotation.py
+++ b/svreader/annotation.py
@@ -204,7 +204,6 @@ class AnnotateReader(VCFReader):
def getHeader(self):
return self.vcf_reader.header
-
def add_annotation_metadata(self):
self.addInfo("SOURCEID", 1, "String",
"The source sv identifier")
@@ -520,7 +519,8 @@ def add_filter_infos_header(reader):
reader.addFilter("ABFREQ", "AB frequency <0.3 for >50% heterosamples")
-def variant_filtration(SVSet, reader):
+def variant_filtration(variants, reader, filter_monomorph=False,
+ filter_callrate=False):
""" Filtering the candidate CNVs according to the following criteria
- non duplicate sites
- variant sites
@@ -534,15 +534,15 @@ def variant_filtration(SVSet, reader):
add_callrate_infos_header(reader)
add_filter_infos_header(reader)
- for sv in SVSet:
+ for sv in variants:
info = sv.record.info
sv.record.info['CALLRATE'] = sv.call_rate(13)
sv.record.info['VARIANTCALLRATE'] = sv.variant_call_rate(13)
- if sv.call_rate(13) < 0.75:
+ if sv.call_rate(13) < 0.75 and filter_callrate:
sv.filter.add("CALLRATE")
- if not sv.polymorph():
+ if not sv.polymorph() and filter_monomorph:
sv.filter.add("MONOMORPH")
- if 'NONDUPLICATEOVERLAP' in info and info['NONDUPLICATEOVERLAP'] > 0.7:
+ if 'NONDUPLICATEOVERLAP' in info and info['NONDUPLICATEOVERLAP'] > 0.8:
sv.filter.add("OVERLAP")
if "DUPLICATESCORE" in info is not None and info['DUPLICATESCORE'] > -2:
sv.filter.add("DUPLICATE")
@@ -559,7 +559,7 @@ def AB_filtering(variant_set):
if Heterozygote(s):
valid_AB_freq.append((s.get('AB')[0] > 0.3))
if (len(valid_AB_freq) > 0 and
- sum(valid_AB_freq) < len(valid_AB_freq) / 2):
+ sum(valid_AB_freq) < len(valid_AB_freq) / 2):
sv.filter.add("ABFREQ")
--
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