Matthias De Smet matthdsm
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| #!/usr/bin/env python | |
| # lib | |
| import argparse | |
| import json | |
| import warnings | |
| import numpy as np | |
| import sys |
matthdsm
/ BarcodeCount.wdl
Created
September 16, 2021 12:02
WDL task to count undetermined barcodes in ExtractIlluminaBarcodes output
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| task BarcodeCount { | |
| meta { | |
| description: "Count barcode occurences from Picard ExtractIlluminaBarcodes output" | |
| } | |
| parameter_meta { | |
| run_barcode: {help: "Flowcell name"} | |
| barcodes: {help: "Barcodes files generated by ExtractIlluminaBarcodes"} | |
| lane: {help: "Lane number"} | |
| num_cpu: {help: "Number of threads to be used"} |
matthdsm
/ refseq2ucsc.tsv
Last active
November 25, 2022 10:29
RefSeq to UCSC accession mapping from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/GCF_000001405.26_GRCh38_assembly_report.txt
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 2 in line 1.
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| RefSeq UCSC | |
| NC_000001.11 chr1 | |
| NC_000002.12 chr2 | |
| NC_000003.12 chr3 | |
| NC_000004.12 chr4 | |
| NC_000005.10 chr5 | |
| NC_000006.12 chr6 | |
| NC_000007.14 chr7 | |
| NC_000008.11 chr8 | |
| NC_000009.12 chr9 |
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| #dbNSFPv3.4 | |
| [[annotation]] | |
| file="{{dbnsfp}}" | |
| names=["hg19_chr","hg19_pos(1-based)","cds_strand","refcodon","codonpos","codon_degeneracy","Ensembl_geneid","Ensembl_transcriptid","Ensembl_proteinid","LRT_score","LRT_converted_rankscore","LRT_pred","LRT_Omega","MutationTaster_score","MutationTaster_converted_rankscore","MutationTaster_pred","MutationTaster_model","MutationTaster_AAE","MutationAssessor_UniprotID","MutationAssessor_variant","MutationAssessor_score","MutationAssessor_score_rankscore","MutationAssessor_pred","FATHMM_score","FATHMM_converted_rankscore","FATHMM_pred","PROVEAN_score","PROVEAN_converted_rankscore","PROVEAN_pred","Transcript_id_VEST3","Transcript_var_VEST3","VEST3_score","VEST3_rankscore","MetaSVM_score","MetaSVM_rankscore","MetaSVM_pred","MetaLR_score","MetaLR_rankscore","MetaLR_pred","Reliability_index","M-CAP_score","M-CAP_rankscore","M-CAP_pred","REVEL_score","REVEL_rankscore","MutPred_score","MutPred_rankscore","MutPred_protID","MutPred_AAchange","MutPred_Top5features","CADD_raw","C |