Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: (#405) somatic variant qc #407

Open
wants to merge 20 commits into
base: main
Choose a base branch
from
Open

feat: (#405) somatic variant qc #407

Changes from 1 commit
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
ad07ebf
Adding wrapper for somatic variants QC
Jun 24, 2023
94cda27
Adding somatic variant qc pipeline
Jun 25, 2023
bd7b411
Update somatic_variant_checking
Jun 30, 2023
de36370
adding test for somatic_variant_checking
Jul 3, 2023
09d8088
format checking
Jul 3, 2023
73416b0
fixing format
Jul 3, 2023
c30f22e
Finalizing somatic variant checking
Jul 8, 2023
956904f
finalize somatic variants checking
Jul 8, 2023
4ce1159
Fix typo
Jul 8, 2023
1f5b0e0
fixing typo
Jul 8, 2023
e99ef3c
fixing small bugs
Jul 13, 2023
62b6e6f
fix: json format doesn't accept floats starting with .
ericblanc20 Jul 25, 2023
5d5246a
Finalizing somatic variant checking
Jul 27, 2023
64e7b61
Merge branch '405-somatic-variant-qc' of github.com:bihealth/snappy-p…
Jul 27, 2023
4750e75
update mantis enviroment
Jul 27, 2023
e9cb75b
finializing somatic_variant_checking
Aug 2, 2023
e9dbc5e
fixing vep environment
Aug 24, 2023
8d1d2c8
Merge branch 'main' into 405-somatic-variant-qc
giacuong171 Nov 14, 2023
70d5bb0
Merge branch '405-somatic-variant-qc' of github.com:bihealth/snappy-p…
Nov 20, 2023
fdbdfff
make isort happy
Nov 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
finializing somatic_variant_checking
  • Loading branch information
giacuong171 committed Aug 2, 2023
commit e9cb75b3cea118e761039cc394cb078b21b341a5
21 changes: 12 additions & 9 deletions snappy_wrappers/wrappers/somatic_variants_checking/summarize-vcf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,13 +36,17 @@ def get_contigs_from_bed_file(bedfile):


def get_variant_type(ref, alt):
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

As we discussed before: perhaps you want to remove possible - characters in ref & alt before checking their length (this would alleviate problems with admittedly badly encoded variants).
Then you have to consider the case of inserts (len(alt) > len(ref))

ref = ref.replace("-", "")
alt = alt.replace("-", "")
variant_type = "unknown"
if len(ref) == len(alt):
if len(alt) == 1:
return "SNV"
if len(ref) == 1:
variant_type = "snv"
else:
return "ONV"
elif len(alt) < len(ref):
return "indel"
variant_type = "onv"
else:
variant_type = "indel"
return variant_type


def check_sp_read(variant, pos_sample, minimal, limited):
Expand Down Expand Up @@ -70,7 +74,6 @@ def assign_class_snvs(variant, mt_mat):
mt_mat[4] += 1
elif temp in ["G>T", "C>A"]:
mt_mat[5] += 1
return mt_mat


def process_vcf_file(
Expand Down Expand Up @@ -129,14 +132,14 @@ def process_vcf_file(
] += 1

# Need to check multi allelic. Users shouldn't input multi allelic vcf file.
if get_variant_type(variant.REF, variant.ALT[0]) == "SNV":
if get_variant_type(variant.REF, variant.ALT[0]) == "snv":
infor["n_snps"] += 1
infor["mt_classes"] = assign_class_snvs(variant, infor["mt_classes"])
assign_class_snvs(variant, infor["mt_classes"])
elif get_variant_type(variant.REF, variant.ALT[0]) == "indel":
# More for indels
infor["n_indels"] += 1
infor["indels_length"].append(abs(len(variant.REF) - len(variant.ALT[0])))
elif get_variant_type(variant.REF, variant.ALT[0]) == "ONV":
elif get_variant_type(variant.REF, variant.ALT[0]) == "onv":
infor["n_onvs"] += 1
# Gathering information of variants in comparison to hard mapped regions
else:
Expand Down