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tkrahn/gist:484cb64430d5c4cea8a2b86c105318b3

Created April 15, 2019 16:32
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Extracting mtDNA FASTA file from WGS BAM
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gistfile1.txt
# mtDNA allele calling $ FASTA file generation
samtools mpileup -r chrM -u -C 50 -v -f ${REF} ${BAMFILE_SORTED} | bcftools call -O z -v -m -P 0 > chrM_${VCF_FILE}.gz
tabix chrM_${VCF_FILE}.gz
samtools faidx $REF chrM | bcftools consensus chrM_${VCF_FILE}.gz -o ${YSEQID}_mtDNA.fasta
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