bmvdgeijn WASP issues - Githubissues

bmvdgeijn / 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