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agaszmurlo/pileup.sh

Last active July 30, 2020 11:00
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pileup test procedure
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pileup.sh
samtools mpileup --fasta-ref ../../reference/Homo_sapiens_assembly18_chr1_chrM.small.fasta -A -q 0 -Q 0 NA12878.multichrom.md.bam -o samtools.pileup2
samtools mpileup --fasta-ref ../../reference/Homo_sapiens_assembly18_chr1_chrM.small.fasta -B -x -A -q 0 -Q 0 NA12878.multichrom.md.bam > samtools_x.pileup
sed $'s/\t"/\t\\\\"/g' samtools_x.pileup> samtools_x_esc.pileup
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