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Old 01-20-2012, 02:20 PM   #1
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Default Samtools mpileup calls drastically more SNPs with -I

The command:
samtools mpileup -b bams.txt -uDSf human_b36_male.fa | bcftools view -vcg - > var.raw.vcf
where bam.txt is a list of BAM files, outputs a var.raw.vcf file with about 200 lines, and the command finishes almost immediately. The same command with the -I flag has so far outputted 3000 lines and is still going. -I is supposed to suppress indel calling, why is it affecting the number of SNPs called so drastically?
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indel, mpileup, samtools

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