Tweet
The command:
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?
Code:
samtools mpileup -b bams.txt -uDSf human_b36_male.fa | bcftools view -vcg - > var.raw.vcf