Question: (Closed) I can call snps but no indels through bcftools
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gravatar for lemon
12 months ago by
lemon0
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 • 247 views
ADD COMMENTlink modified 12 months ago by h.mon28k • written 12 months ago by lemon0

Hello lemon!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 12 months ago by h.mon28k
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