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bmvdgeijn
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WASP
WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
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Changed output from filter_remapped_reads.py
#122
kwcurrin
opened
4 months ago
0
Is it feasible to use population-level SNP instead of individual sample's variant information?
#121
zhangjy859
opened
8 months ago
2
Error parsing genotype likelihoods
#120
aanderson54
opened
9 months ago
0
No geno_prob files for extract_haplotype_read_counts.py
#119
cybluetree
closed
11 months ago
0
Is WASP suitable for WGBS data?
#118
taolincj
opened
1 year ago
0
VCF to HDF5 Error
#117
PaulinaUrbana
opened
2 years ago
0
error in rule "get_as_counts" / bam2h5.py
#116
azurillandfriend
opened
2 years ago
0
running snp2h5 in the mapping snakemake
#115
azurillandfriend
opened
2 years ago
1
filter_remapped_reads.py with bams created by HISAT2/ other mappers than Bowtie2
#114
azurillandfriend
opened
2 years ago
2
Incomplete h5 files with snp2h5
#113
brewert2
closed
2 years ago
0
running filter_remapped_reads.py on multiple samples all get empty bam files
#112
wdlv
closed
2 years ago
0
Whole genome sequencing data
#111
maggietsui
opened
2 years ago
1
find_intersecting_snps.py: for pair in product(new_reads[0][group], new_reads[1][group]): IndexError: list index out of range
#110
jegalle
opened
2 years ago
1
Represent phased blocks in VCF file
#109
ramesh8v
opened
2 years ago
1
Minor typo in Snakefile
#108
rschwess
opened
3 years ago
0
find_intersecting_snps.py
#107
LunaPatton
opened
3 years ago
3
filter_remapped_reads.py
#106
p4rkerw
opened
3 years ago
2
Small sample size
#105
montenegrina
opened
3 years ago
3
find_intersecting_snps.py outputting sam files rather than bam files
#104
gbloeb
opened
3 years ago
2
VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated
#103
gbloeb
opened
3 years ago
0
CHT Snakemake workflow getting stuck at adjust_read_counts
#102
adamturner1
opened
3 years ago
0
Many reads discarded due to remapping with different CIGAR
#101
hrayjones
closed
3 years ago
6
Missing step in CHT readme?
#100
Zepeng-Mu
opened
3 years ago
0
about NAs and 0s in CHT step 6 "extract_haplotype_read_counts"
#99
lw157
opened
4 years ago
0
Will rmdup_pe.py behave normally if one mate from a read pair is removed?
#98
boxiangliu
closed
4 years ago
1
speedup for fit_as_coefficients?
#97
lw157
closed
4 years ago
2
update_total_depth takes too long
#96
lw157
closed
4 years ago
4
constructing input files for pairwise eQTL testing
#95
ghost
opened
4 years ago
5
find_intersecting_snps.py taking longer than expected?
#94
rwomersley
opened
4 years ago
3
find_intersecting_snps.py : WARNING: unable to read from file
#93
daphniamagna
opened
4 years ago
4
zlib version check suggestion
#92
nicolasrochette
closed
4 years ago
1
snp2h5 reads vcfs as empty
#91
snaqvi1990
closed
4 years ago
5
Could not find test snp
#90
SaideepGona
opened
4 years ago
1
Incorrect matching during Step2 of CHT
#89
katiearacena
closed
4 years ago
5
Obtaining phased genotype data
#88
katiearacena
opened
4 years ago
1
No module named 'util'
#87
viraj-rapolu
opened
4 years ago
1
find_intersecting_snps.py does not handle paired-end read correctly
#86
orionzhou
opened
5 years ago
3
Duplicated rows in example input files and eQTL mapping pipeline
#85
liangyy
opened
5 years ago
7
HDF5 vs text-based
#84
robinweide
opened
5 years ago
0
Running WASP per chromosome
#83
arielmadr
opened
5 years ago
5
Error in bam2h5.py
#82
danliangunc
opened
5 years ago
0
find_intersecting_snps.py input files
#81
Liying1996
closed
5 years ago
0
- fixing bug D and I CIGAR
#80
MingshiGao
closed
5 years ago
0
ind_intersecting_snps.py error
#79
raungar
closed
2 years ago
2
Handling of partially mapped reads not implemented
#78
feliciecos
opened
5 years ago
16
find_intersecting_snps.py possible error in reporting remap reads
#77
kwcurrin
opened
6 years ago
9
Fixes and improvements to mapping pipeline
#76
gmcvicker
closed
6 years ago
0
snp2h5 no longer supports matching chromosomes regardless of "chr" prefix
#75
kwcurrin
closed
6 years ago
2
WARNING: vcf.c:262: some genotypes are unphased (delimited with '/' instead of '|')
#74
sorrowripple
opened
6 years ago
1
Run the example extract_haplotype_read_counts, error IOError
#73
yjzhang1020
opened
6 years ago
1
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