secastel phaser issues - Githubissues

secastel / phaser

phasing and Allele Specific Expression from RNA-seq

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Recommendations for running phaser with just the rnaseq data

#82 aswathyseb closed 2 weeks ago
3
phaser annotate module is still py2.7?

#81 FunongLuo closed 2 weeks ago
2
Port phaser to Python 3 via 2to3

#80 pettyalex closed 2 months ago
4
parameter '--no_gw_phase 0'

#79 shiwobu closed 1 year ago
2
Error in using phaser_gene_ae.py

#78 c-nabokov opened 1 year ago
5
trying to locate phASER_GTEx_v8_merged.vcf.gz for phaser_cis_var.py (phaser-pop)

#77 7ehuang opened 1 year ago
0
phaser.py requires pysam

#76 davetang closed 2 years ago
1
Container

#75 RenzoTale88 closed 2 years ago
3
Issues with phaser-pop

#74 lilyjiang94 closed 2 years ago
2
software is suitable for ChIP-seq data

#73 TaoHJiang closed 2 years ago
4
version of phaser on github

#72 ponomarevsy opened 2 years ago
0
Error running phaser

#71 Arkosen closed 2 years ago
3
question regarding input vcf

#70 lyj95618 opened 2 years ago
4
phASER error

#69 woshiyangsi closed 3 years ago
0
what kind of vcf file i can use?

#68 woshiyangsi closed 3 years ago
0
Advice on how to run phASER with RNA-seq data only and posed genotypes of parents

#67 apfuentes opened 3 years ago
1
Retrieve parent of origin for haplotypes

#66 vilperte closed 3 years ago
1
phaser_gene_ae output with 0 Count?

#65 deb0612 opened 3 years ago
1
FATAL ERROR: No heterozygous sites that passed all filters were included in the analysis

#64 deb0612 closed 3 years ago
19
TypeError: a bytes-like object is required, not 'str

#63 deb0612 closed 3 years ago
3
How to use phaser without vcf file

#62 darenzhao opened 3 years ago
0
check_dependency("bedtools") == False

#61 deb0612 closed 3 years ago
0
Advice on phasging protocole with RNASeq only

#60 mariabernard closed 3 years ago
3
tabix error due to pandas behavior in python 2.7

#59 daniel-munro opened 4 years ago
0
no alignment score value found in reads

#58 molecularsensei opened 4 years ago
5
cannot run phASER to my aligned data

#57 x811zou opened 4 years ago
5
No alignment score in BAM file

#56 rahulk87 closed 4 years ago
2
fails after omitting blacklist arg to allow progress

#55 vjcitn closed 5 years ago
1
example fails on blacklist intervals

#54 vjcitn closed 5 years ago
1
subprocess.CalledProcessError

#53 msubirana closed 4 years ago
1
phASER duplicates VCF meta-information FORMAT lines in output VCF

#52 tinyheero closed 5 years ago
1
RSLVD?: Invalid literal during cutoff: " "

#51 LillianZ closed 4 years ago
2
Prior population phasing with or without WGS?

#50 snaqvi1990 opened 5 years ago
2
Phaser freezing after retrieving reads

#49 clarepacini closed 5 years ago
3
Update README.md

#48 everestial closed 2 months ago
0
Additional Commits

#47 everestial closed 5 years ago
9
Update phaser.py

#46 everestial closed 6 years ago
0
Update phaser.py

#45 everestial closed 4 years ago
0
Memory issue on phaser

#44 everestial closed 4 years ago
4
Issues with the reference genome update（hg19 to hg38）

#43 clsteam closed 6 years ago
1
Allele specific expression on multiple samples

#42 mbosio85 opened 6 years ago
4
Issues with VCF merge after running phaser

#41 everestial opened 6 years ago
7
Loss of AD/DP info after phasing

#40 mbosio85 closed 6 years ago
3
Question on out_prefix.vcf.gz

#39 JohnMCMa closed 4 years ago
1
Get all possible haplotypes for a particular gene

#38 evigorito closed 4 years ago
3
problem when running phaser

#37 jfertaj closed 6 years ago
18
Subprocess now checks call return values

#36 agraubert closed 6 years ago
0
Replaced usage of quit() with sys.exit(1)

#35 agraubert closed 6 years ago
1
Summed DNA and RNA counts in allelic_counts output file?

#34 freerkvandijk closed 4 years ago
5
phaser_gene_ae only compatible with v1.0.0+, I'm using v1.0.0

#33 npklein closed 6 years ago
1