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| bcftools view -V indels merged.raw.vcf.gz | setGT.py | bcftools view -a | bcftools filter -e 'GT="het"' -S . | bcftools view -i 'F_PASS(GT!="mis")>0.9' | bcftools view -c 1 | bcftools norm -f ../reference/Mycobacterium_abscessus.7396_7_44.dna.toplevel.fa | bcftools view -Oz -o merged.filt.vcf.gz |
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