Commit b77977e1 authored by van den Berg's avatar van den Berg
Browse files

Add test for RUNX1 insertion

This tests the fix for #issue-11, which was resolved by a new upstream release
of the gmap aligner. The same upstream release also fixes #issue-12.
parent 3610caf9
Pipeline #3831 passed with stages
in 46 minutes and 54 seconds
{
"settings": {
"flt3_bwa_index": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-flt3-index/flt3-001.fa",
"kmt2a_fasta": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-kmt2a-index/kmt2a-213.fa",
"genome_star_fusion_lib": "/exports/sasc-testing/fixtures/HAMLET/deps/data/GRCh38_gencode_v31_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir",
"flt3_start": 1787,
"relative_gene_name": "HMBS",
"expression_gtf": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_gencode.gtf",
"expression_bed": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_gencode.flat.bed",
"vcf_gonl": "/exports/sasc-testing/fixtures/HAMLET/deps/data/gonl.grch38.sorted.filtered.snps_indels.r5.vcf.gz",
"kmt2a_start": 406,
"annotation_refflat": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_gencode.refFlat",
"kmt2a_end": 4769,
"kmt2a_name": "KMT2A-213",
"bed_variant_hotspots": "/exports/sasc-testing/fixtures/HAMLET/deps/data/hotspots_genome.bed",
"exon_names": [
"MECOM:169146722-169147734"
],
"exon_min_ratio": 0.1,
"ref_annot_goi": "/exports/sasc-testing/fixtures/HAMLET/deps/data/Homo_sapiens.GRCh38.77.goi-extended.gtf",
"flt3_end": 2024,
"genome_fasta": "/exports/sasc-testing/fixtures/HAMLET/deps/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa",
"fasta_vep": "/exports/sasc-testing/fixtures/HAMLET/deps/vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz",
"flt3_name": "FLT3-001",
"cache_vep": "/exports/sasc-testing/fixtures/HAMLET/deps/vep/ensembl-vep/cache_dir/",
"ref_id_mapping": "/exports/sasc-testing/fixtures/HAMLET/deps/data/id_mappings.tsv",
"kmt2a_bwa_index": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-kmt2a-index/kmt2a-213.fa",
"flt3_fasta": "/exports/sasc-testing/fixtures/HAMLET/deps/data/bwa-flt3-index/flt3-001.fa",
"rrna_refflat": "/exports/sasc-testing/fixtures/HAMLET/deps/data/ucsc_rrna.refFlat",
"ref_amplicons": "/exports/sasc-testing/fixtures/HAMLET/deps/data/amplicons.bed",
"genome_gmap_index": "/exports/sasc-testing/fixtures/HAMLET/deps/data/gmap-genome-index/GCA_000001405.15_GRCh38_no_alt_analysis_set",
"run_name": "hamlet-hiseq2500",
"vcf_1kg": "/exports/sasc-testing/fixtures/HAMLET/deps/data/1KG.phase3.GRCh38.with_chr.vcf.gz",
"transcripts_bed": "/exports/sasc-testing/fixtures/HAMLET/deps/data/transcripts.bed",
"fusioncatcher_data": "/exports/sasc-testing/fixtures/HAMLET/deps/fusioncatcher/human_v98/",
},
"samples": {
"7075-04-001-002": {
"read_groups": {
"rg_1": {
"R1": "test/data/fastq/7075-04-001-002-RUNX1_R1.fastq.gz",
"R2": "test/data/fastq/7075-04-001-002-RUNX1_R2.fastq.gz",
}
}
}
}
}
......@@ -131,7 +131,6 @@
- name: test-TET2-insertion-config
tags:
- integration
- new
command: >
snakemake -rp
--snakefile includes/snv-indels/Snakefile
......@@ -150,3 +149,18 @@
- "chr4\t105259623\t.\tA\tC"
- "chr4\t105259624\t.\tC\tT"
- "chr4\t105259626\t.\tT\tG"
- name: test-RUNX1-insertion
tags:
- integration
command: >
snakemake -rp
--snakefile includes/snv-indels/Snakefile
--configfile test/data/config/test-RUNX1-insertion.config
--verbose
--use-singularity
"7075-04-001-002/snv-indels/7075-04-001-002.raw.vcf.gz"
files:
- path: "7075-04-001-002/snv-indels/7075-04-001-002.raw.vcf.gz"
contains:
- "chr21\t34792223\t.\tA\tACGTCGCTCTGGTT"
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