Question: (Closed) I can call snps but no indels through bcftools
gravatar for lemon
22 months ago by
lemon0 wrote:
     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
snp sequence assembly • 401 views
ADD COMMENTlink modified 22 months ago by h.mon31k • written 22 months ago by lemon0

Hello lemon!

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ADD REPLYlink written 22 months ago by h.mon31k
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