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NBISweden
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GenErode
GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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Update config_plugin_dardel.yaml
#84
Estel-Kitsune
opened
2 months ago
0
Update configuration files for slurm executor plugin profiles
#83
verku
closed
2 months ago
0
Updates for GenErode version 0.6.1
#82
verku
closed
2 months ago
0
Updates to slurm profile for Snakemake 8 slurm executor plugin
#81
verku
closed
2 months ago
0
Upgrade to snakemake version 8 with plugin profile
#80
verku
closed
2 months ago
0
Update to Snakemake version 8 and other software updates
#79
verku
closed
2 months ago
0
Add subsampling depth to merged VCF file path name
#78
verku
opened
2 months ago
0
Make it possible to use tab- or comma-separated metadata files
#77
verku
opened
3 months ago
0
Enable BAM and VCF files as input for GenErode
#76
verku
opened
5 months ago
0
Check that last line of GERP and VCF file is processed by gerp_derived_alleles.py
#75
verku
opened
5 months ago
0
Add note to documentation about MapDamage2 rescale creating biases
#74
verku
opened
6 months ago
0
Fix minimum overlap for read merging in fastP
#73
verku
opened
7 months ago
0
Update Snakemake to v8
#72
verku
closed
2 months ago
1
Double check if sorting of BAM and VCF files is strictly necessary
#71
verku
opened
7 months ago
0
ANGSD error estimation
#70
verku
opened
7 months ago
0
Check how slurm profile handles group jobs
#69
verku
closed
2 months ago
1
filter_mpile.py does not keep first and last nucleotide in a read
#68
verku
opened
7 months ago
0
Update gerp_derived_alleles.py to work with phased genotypes
#67
verku
opened
7 months ago
0
fastp cannot autodetect NovaSeqXPlus for automatic polyG trimming
#66
verku
closed
7 months ago
1
Mapping of historical samples: make bwa aln parameter -n available in config file
#65
verku
opened
8 months ago
0
Add optional (?) second deduplication step between final merging and indel realignment for historical samples
#64
verku
opened
8 months ago
0
Update repeatmodeler to version 2.0.4 to handle large genomes
#63
verku
closed
10 months ago
0
missingness_filtered_vcf_multiqc fails when running GenErode only with modern or only with historical samples
#62
verku
closed
7 months ago
0
RepeatModeler fails on big genomes
#61
mariannedehasque
closed
7 months ago
3
Add GenErode to Workflowhub
#60
verku
opened
11 months ago
0
Move rescaling to gerp rule and update documentation
#59
verku
closed
11 months ago
0
Version 0.6.0 updates
#58
verku
closed
7 months ago
1
Optional removal of sex chromosomes from VCF files
#57
verku
closed
10 months ago
0
Fix typo for temporary json file in fastp_historical
#56
verku
closed
7 months ago
0
Filtering for biallelic sites does not remove sites with fixed derived variants
#55
verku
opened
11 months ago
1
Implement splitting VCF files into autosomes and sex chromosomes
#54
verku
closed
7 months ago
0
Replace rescale_gerp rule with gerpcol parameter "-s"
#53
verku
closed
7 months ago
1
Check cutoffs
#52
verku
closed
1 year ago
0
Fastqc Memory issues
#51
lored322
closed
7 months ago
1
Problems running pipeline in Uppmax using the rhinos test dataset and slurm profile
#50
apfuentes
closed
2 months ago
2
rule multiqc_historical_raw: Stuck on 'Searching'
#49
johannanvs
opened
1 year ago
13
rule 7_mlrho dependant on final 3.1 bam.bai temporary file
#48
lored322
closed
7 months ago
2
pipeline stuck at 'Building DAG of jobs'
#47
ndussex
closed
1 year ago
5
GERP scores - size of chunks for derived alleles calculations
#46
ndussex
closed
1 year ago
4
Repeatmasker fails when attempting to zip the *cat file
#45
verku
closed
1 year ago
2
Wrong input file in rule index_realigned_bams in workflow 3.1_bam_rmdup_realign_indels.smk?
#44
johannanvs
closed
1 year ago
1
Add slurm profile to repository that works with Snakemake version in the conda environment
#43
verku
closed
2 months ago
0
Bug fix to ensure functionality
#42
verku
closed
1 year ago
0
Missingness filter fails when filtering for sites with zero missing data or when including all sites
#41
verku
closed
1 year ago
0
Extract SNPs prior to VCF merging
#40
verku
closed
1 year ago
0
individual vcfs merging failing
#39
ndussex
closed
1 year ago
14
Add code to edit GenErode pipeline report
#38
verku
closed
10 months ago
1
Update the WIKI
#37
verku
closed
1 year ago
0
Add slurm profile config.yaml
#36
verku
closed
1 year ago
0
Bug fixes
#35
verku
closed
1 year ago
0
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