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EPPIcenter
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mad4hatter
https://eppicenter.github.io/mad4hatter/
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update readme apptainer instructions
#111
bgpalmer
closed
1 year ago
0
Make sure that column names are consistent across output files
#110
andres-ad
closed
1 year ago
1
add masking to pseudocigar with agreed syntax
#109
andres-ad
closed
1 year ago
0
Pipeline restructure
#108
bgpalmer
closed
1 year ago
0
Make sure alignments work for all reference file fastas
#107
bgpalmer
opened
1 year ago
0
Keep locus column in microhap table
#106
manuelgug
closed
1 year ago
0
Varying order of positions and variants for multiallelic loci in resmarkers_microhap_table.txt
#105
manuelgug
closed
1 year ago
2
"novel" mutations in our drug R data that are likely bioinformatic errors
#104
jbriggs7
closed
1 year ago
0
if there is only one demultiplexed amplicon with average F+R reads sh…
#103
bgpalmer
closed
1 year ago
0
Resmarkers aad
#102
bgpalmer
closed
1 year ago
1
Use cutadapt json
#101
bgpalmer
closed
1 year ago
1
new reference that has all Plasmodium genomes
#100
andres-ad
closed
1 year ago
1
adopt pseudocigar syntax from Neafsey lab
#99
andres-ad
closed
1 year ago
3
microhaplotype output missing column name in resmarkers_aad
#98
andres-ad
closed
1 year ago
1
empty dataframes in resmarkes
#97
andres-ad
closed
1 year ago
0
Add SNP coordinates to resmarker output
#96
andres-ad
opened
1 year ago
2
postprocessing qc outputs not outputting
#95
andres-ad
closed
1 year ago
0
long amplicons
#94
andres-ad
opened
1 year ago
1
homopolymer
#93
andres-ad
closed
1 year ago
1
insertions in pseudo cigar
#92
andres-ad
closed
1 year ago
1
selfConsist
#91
andres-ad
closed
1 year ago
1
vcf
#90
andres-ad
opened
1 year ago
0
non-listed SNPs
#89
andres-ad
closed
1 year ago
1
SNPs that show in more than 1 amplicon
#88
andres-ad
opened
1 year ago
1
tandem repeat and homopolymer masking
#87
andres-ad
closed
1 year ago
0
Non-pf sequences
#86
andres-ad
opened
1 year ago
1
Non overlapping truncation length
#85
andres-ad
opened
1 year ago
1
Insertions and deletions in resmarkers
#84
andres-ad
opened
1 year ago
0
Change names of R files to make them more intuitive (e.g. bcf tools is not used)
#83
andres-ad
closed
1 year ago
0
clean and finish annotating postdada_rearrange from resmarker_aad if and when merged
#82
andres-ad
closed
1 year ago
0
Annotate resistance marker module in resmarker_aad branch when merged
#81
andres-ad
closed
1 year ago
0
Look at the new code Andres wrote for postdada and resmarkers and merge if good
#80
andres-ad
closed
1 year ago
0
Vcf4
#79
bgpalmer
closed
1 year ago
0
postproc changes
#78
bgpalmer
closed
1 year ago
0
add back sample median reads per pool (#76)
#77
bgpalmer
closed
1 year ago
0
add back `Sample Median Reads per Pool` to quality report
#76
bgpalmer
closed
1 year ago
0
Pf coverage
#75
bgpalmer
closed
1 year ago
0
Changes for v0.0.10
#74
bgpalmer
closed
1 year ago
0
fix outputs and visualizations
#73
manuelgug
closed
1 year ago
2
fixing graphs in the QC htmls that are created
#72
jbriggs7
closed
1 year ago
1
Changes for v0.0.9
#71
bgpalmer
closed
1 year ago
0
Norm.reads.allele - column needs to be removed from allele_data output
#70
jbriggs7
closed
1 year ago
1
add to sample_coverage file the # of reads that map to Pf
#69
jbriggs7
closed
1 year ago
1
add column names to sample coverage and amplicon coverage output files
#68
jbriggs7
closed
1 year ago
1
Changes for v0.0.8
#67
ghost
closed
1 year ago
0
Fix for non overlaps
#66
ghost
closed
1 year ago
0
Changes for v0.0.5
#65
ghost
closed
1 year ago
0
Updates for v0.0.4
#64
ghost
closed
1 year ago
0
Updates for v0.0.3
#63
ghost
closed
1 year ago
0
add argparse version of create_refseq.R
#62
ghost
closed
1 year ago
0
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