1 2 3 4 5 6 7 8 9 ref: A A T T C C G G…… alt: A A A T T C C G G……
if my sequence act as above, then i use bcftools to call variance, it comes results as many snps in position 3, position 5, position 7……but no indels, however, actually it should be an indel (insert) at position 1 or 2.
I did the whole genome call variance, all results are snps but no indels, could anybody tell me how to solve this problem?
the commond line I used is as follows:
bcftools mpileup -Ou -f /annovar/db/a.fa /annovar/adb/C13.bam | \ bcftools call -Ou -mv | \ bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > C13.flt.vcf