22 lines
974 B
Plaintext
22 lines
974 B
Plaintext
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To extract HLA alleles and variants
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./hisatgenotype_extract_vars.py --base codis --inter-gap 30 --intra-gap 50 --min-var-freq 0.1
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./hisatgenotype_extract_vars.py --base hla --locus-list A --inter-gap 30 --intra-gap 50 --min-var-freq 0.1
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To build genotype genome
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./hisatgenotype_build_genome.py genome.fa genotype_genome -p 3 --verbose
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For DNA fingerprinting
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./hisatgenotype_locus.py --verbose --base codis --locus-list D13S317 --fragment-len 200 --no-assembly --debug paired
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To run HISAT-genotype
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./hisatgenotype_locus.py --base hla --locus-list A --simulate-interval 10 --perbase-errorrate 0.3 --perbase-snprate 0.1 --num-editdist 2 --debug paired
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for i in `ls -l ILMN/NA128*1.fq.gz | awk '{print $NF}' | cut -d'/' -f2 | cut -d'.' -f1`; do echo $i; ./hisatgenotype_locus.py --locus-list A --aligner-list hisat2.graph --num-editdist 2 --reads ILMN/$i.extracted.1.fq.gz,ILMN/$i.extracted.2.fq.gz --assembly-base assembly_graph_$i 2> $i.tmp; done
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