I got my sequence data, and i want to call its snp and indel when reference genome exists. the commond i used is as follows:
bcftools mpileup -Ou -f /annovar/Gadb/Ga.fa /annovar/Gadb/0613.bam | \ bcftools call -Ou -mv | \ bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > 0613.flt.vcf
this is a whole genome, and it should contain indels. but the results i got form this commond only contain snps , however, no indels.
could anyone help me solve this problem?