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Issues list

Enable AF reporting for both gnomad/exac VCFs, whether GRCh37/GRCh38
#92 opened Oct 25, 2016 by ckandoth
@andurill
3
More careful whitelisting of known somatic variants
#102 opened Dec 8, 2016 by ckandoth
@ckandoth
2
Getting 'uninitialized value' error
#135 opened Aug 25, 2017 by ckandoth
@ckandoth
2
FILTER tags of same variant from different samples are being merged bug
#142 opened Sep 28, 2017 by ckandoth
@ckandoth
Add support for the VEP plugins LoF and LoFtool enhancement
#145 opened Oct 30, 2017 by alexpenson
@ckandoth
Handle new start_retained_variant seen in a VEP v91 run
#158 opened Mar 1, 2018 by ckandoth
@ckandoth
1
Obtain variant allele fraction from VCF
#171 opened May 31, 2018 by bioinfo-dirty-jobs
@ckandoth
4
WT1 missing from isoform_overrides_uniprot_from_biomart_91 and isoform_overrides_uniprot
#173 opened Jun 12, 2018 by rhshah
@inodb
4
Does vcf2maf work for Mac OS?
#176 opened Jun 21, 2018 by lemuelsoh
1
vcf2maff resuts on varsccan
#178 opened Jul 5, 2018 by bioinfo-dirty-jobs
Run vcf2maf for bcftools merged vcf
#180 opened Jul 17, 2018 by DadongZ
WARNING: 51499 : Use of uninitialized value in subtraction (-)
#182 opened Jul 18, 2018 by DadongZ
1
retain info from FORMAT field vcf2maf
#184 opened Jul 19, 2018 by anabbi
2
Problem in annotating mice vcf
#186 opened Aug 6, 2018 by banerjeeshayantan
Problem with running maf2vcf using GRch38 as reference fasta
#187 opened Aug 7, 2018 by Frank-LSY
3
maf2vcf :how was the result of FILTER in the vcf files computed?
#192 opened Sep 12, 2018 by paradoxechen
Failed to run vcf2maf for a vcf file cleaned with vcf2vcf
#194 opened Sep 22, 2018 by wisekh6
@ckandoth
1
Add support for LoFreq VCFs
#196 opened Oct 4, 2018 by ckandoth
@ckandoth
--ref-fasta is missing or empty
#200 opened Oct 25, 2018 by cegg
@ckandoth
14
vcf2vcf genotyping using bam input
#202 opened Nov 6, 2018 by fpbarthel
@ckandoth
1
ERROR: Failed to run the VEP annotator!
#204 opened Dec 14, 2018 by neilihrke
@ckandoth
8
New VEP does not handle Delly SV VCFs
#208 opened Dec 26, 2018 by ckandoth
@ckandoth
maf2vcf.pl: multiple FILTER tags should be semicolon separated
#209 opened Dec 30, 2018 by soccin
@ckandoth
2
Infer Frame from breakend format for SVs
#217 opened Mar 16, 2019 by ckandoth
@ckandoth
SOMATIC INFO field on VCF
#218 opened Mar 18, 2019 by caaespin
ProTip! Adding no:label will show everything without a label.