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indel detection dindel test mpileup ./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup MM140738JS.bam -v -u > test.vcf 10:72358747 samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam ./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup -uf /lgc/datasets/hg19/new/hg19/hg19.fa MM140738JS.bam | ./samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools call -mv > var.raw.vcf Read more…