Add yallhap test data for Y-chromosome haplogroup classification#1842
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trianglegrrl wants to merge 1 commit intonf-core:modulesfrom
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Add yallhap test data for Y-chromosome haplogroup classification#1842trianglegrrl wants to merge 1 commit intonf-core:modulesfrom
trianglegrrl wants to merge 1 commit intonf-core:modulesfrom
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Adds test data for the yallhap module (Y-chromosome haplogroup classification tool).
Files added
Reference data (
genome/yallhap/):yfull_tree.json- YFull phylogenetic tree for haplogroup classificationybrowse_snps_grch37.csv- YBrowse SNP database with GRCh37 coordinatesTest samples (subsetted from ancient Kennewick Man data):
illumina/bam/test_ydna.bam+.bai- Y-chromosome BAM (classifies as Q-M930)illumina/vcf/test_ydna.vcf.gz+.tbi- Y-chromosome VCF (classifies as Q-L472)Usage
These files support testing the yallhap nf-core module for both VCF and BAM input modes:
yallhap classify test_ydna.vcf.gz --tree yfull_tree.json --snps ybrowse_snps_grch37.csvyallhap classify test_ydna.bam --tree yfull_tree.json --snps ybrowse_snps_grch37.csvRelated: https://github.com/nf-core/modules (yallhap module PR)