ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data

ylab-hi/ScanNeo Issues

Errors about parsing the VEP annotation output file (tmp_vcf)
Updated 2 years ago2
Example data set
Updated 2 years ago
anno phase not working
Closed 2 years ago7
vep_install --> perl INSTALL.pl
Closed 2 years ago2
Downstream.pm should be installed vep's INSTALL.pl
Updated 2 years ago
Update Wildtype.pm from pVACtools
Updated 2 years ago
PyVCF is deprecated for python3
Closed 2 years ago
VEP cache/plugin directory option not implemented
Closed 2 years ago2
KeyError 'mm39_ref'
Closed 2 years ago2
PyVCF
Updated 2 years ago3
Got a warning: Warning: There was a mismatch between the actual wildtype amino acid and the expected amino acid
Updated 3 years ago
transIndel_call.py ,StopIteration
Closed 3 years ago1
No .bwa.bam generated
Closed 3 years ago2
IOError: [Errno 9] Bad file descriptor when calling IEDB analysis
Closed 4 years ago6
empty vcf file in step2 anno
Closed 4 years ago2
indel.bam not being created
Closed 3 years ago3
pysam module not found
Closed 4 years ago3
Where can I access the LNCaP RNA-seq data
Closed 4 years ago1
why does ScanNeo realign with bwa?
Closed 4 years ago1