Skip to content

Update vcfpy dependency to a newer version #84

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

Open
susannasiebert wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Update vcfpy dependency to a newer version #84

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6212dd6
Update vcfpy dependency to a newer version and update test data
susannasiebert Jan 30, 2026
d19f75c
Add support for Python 3.12
susannasiebert Jan 30, 2026
fd59b98
Switch from deprecated distutils function to distutils-strtobool package
susannasiebert Jan 30, 2026
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
2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]

@chrisamiller chrisamiller Jun 30, 2026

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

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

Should we be bumping this list to support later versions (up to 3.14) now?

@susannasiebert susannasiebert Jun 30, 2026

Copy link
Copy Markdown
Collaborator Author

Choose a reason for hiding this comment

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

Sure. We might run into some dependency incompatibility so we'd need to decide how to best resolve them.


steps:
- uses: actions/checkout@v2
Expand Down
3 changes: 2 additions & 1 deletion setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,11 +16,12 @@
]
},
install_requires=[
'vcfpy==0.12.3',
'vcfpy==0.13.8',

@chrisamiller chrisamiller Jun 30, 2026

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

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

should we bump this to the newest (0.14.2) at this point?

@susannasiebert susannasiebert Jun 30, 2026

Copy link
Copy Markdown
Collaborator Author

Choose a reason for hiding this comment

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

I feel like there was some reason to pin this version but I don't remember. I think I was trying to keep it in line with what pVACtools uses (which isn't really required). There might also be some incompatibility with python versions and/or other dependencies.

'pysam',
'pandas',
'gtfparse==1.3.0',
'testfixtures',
'distutils-strtobool',
],
classifiers=[
'Development Status :: 5 - Production/Stable',
Expand Down
153 changes: 153 additions & 0 deletions tests/test_data/af_number_1.bam-readcount.readcount.vcf
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion tests/test_data/existing_sample.genotype.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,4 +79,4 @@
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395
22 18644673 . C T . . CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
22 18644673 . C T . . CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
2 changes: 1 addition & 1 deletion tests/test_data/hom_ref.readcount.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -150,4 +150,4 @@
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr22 36265781 . T G . PASS AC=1;AF=0.25;AN=4;ECNT=1;HCNT=18;MAX_ED=.;MIN_ED=.;NLOD=30.75;TLOD=16.26;set=mutect;CSQ=G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000319136|protein_coding|7/7||||1260|993|331|G|ggT/ggG|||1||1|HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397278|protein_coding|6/6||||1174|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397279|protein_coding|6/7||||1043|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000422471|nonsense_mediated_decay|||||||||||4108|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000422706|protein_coding|6/6||||1152|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000426053|protein_coding|5/5||||1059|891|297|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000427990|protein_coding|||||||||||466|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLR,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000431184|nonsense_mediated_decay|||||||||||4148|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMVVVLNAVEFETLFLNFK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000433768|protein_coding|||||||||||4137|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000438034|protein_coding|||||||||||4106|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRSTLSQPLFSCSRRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLT,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000439680|nonsense_mediated_decay|||||||||||4082|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1:DP:ADF:ADR 0/0:207,5:0.02358:0:4:0.0:4478,60:88:79:212:108,0:99,5 0/1:341,42:0.10966:1:61:0.016:8708,1130:190:119:383:.:.
chr22 36265781 . T G . PASS AC=1;AF=0.25;AN=4;ECNT=1;HCNT=18;MAX_ED=.;MIN_ED=.;NLOD=30.75;TLOD=16.26;set=mutect;CSQ=G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000319136|protein_coding|7/7||||1260|993|331|G|ggT/ggG|||1||1|HGNC|HGNC:618||||||||||||||||||||||MRFKSHTVELRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397278|protein_coding|6/6||||1174|945|315|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397279|protein_coding|6/7||||1043|945|315|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000422471|nonsense_mediated_decay|||||||||||4108|1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000422706|protein_coding|6/6||||1152|945|315|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000426053|protein_coding|5/5||||1059|891|297|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000427990|protein_coding|||||||||||466|1|cds_end_NF||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLR,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000431184|nonsense_mediated_decay|||||||||||4148|1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMVVVLNAVEFETLFLNFK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000433768|protein_coding|||||||||||4137|1|cds_end_NF||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000438034|protein_coding|||||||||||4106|1|cds_end_NF||HGNC|HGNC:618||||||||||||||||||||||MRFKSHTVELRSTLSQPLFSCSRRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLT,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000439680|nonsense_mediated_decay|||||||||||4082|1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1:DP:ADF:ADR 0/0:207,5:0.02358:0:4:0.0:4478,60:88:79:212:108,0:99,5 0/1:341,42:0.10966:1:61:0.016:8708,1130:190:119:383:.:.
8 changes: 4 additions & 4 deletions tests/test_data/indel_mode.bam_readcount.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_NJ-HCC1395-HCC1395
6 41754573 . C CCTT . . CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1%3Ac.861_862insCTT|ENSP00000404911.1%3Ap.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF:ADF:ADR 0/1:76:13,9,28,26:36:2:22,52:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS:0.68421:13,26:9,26
6 43250725 . GGAA G . . CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4%3Ac.2248_2250delGAA|ENSP00000259750.4%3Ap.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF 0/1:0:43,47,54,56:34:2:0,0:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS:0
22 16228619 . T C . . CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1%3An.909T>C|||| GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC 1/1:0,5:42:2:7:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60
22 18644673 . C T . . CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
6 41754573 . C CCTT . . CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1:c.861_862insCTT|ENSP00000404911.1:p.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF:ADF:ADR 0/1:76:13,9,28,26:36:2:22,52:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS:0.68421:13,26:9,26
6 43250725 . GGAA G . . CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4:c.2248_2250delGAA|ENSP00000259750.4:p.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF 0/1:0:43,47,54,56:34:2:0,0:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS:0
22 16228619 . T C . . CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1:n.909T>C|||| GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC 1/1:0,5:42:2:7:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60
22 18644673 . C T . . CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD 0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
Loading