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jodyphelan/minimap2

Created July 23, 2020 15:03
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minimap2
wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa
printf "Chromosome\t5\tX\tT\n" > snp.txt
printf "Chromosome\t50000\tX\tT\n" >> snp.txt
seqtk mutfa H37Rv.fa snp.txt >mutant.fa
# My current command
minimap2 H37Rv.fa mutant.fa --cs | sort -k6,6 -k8,8 | paftools.js call -l 100 -L 100 -f H37Rv.fa -s test -
# With -x asm5
minimap2 H37Rv.fa mutant.fa --cs -x asm5 | sort -k6,6 -k8,8 | paftools.js call -l 100 -L 100 -f H37Rv.fa -s test -
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