why I used bcftools mpilup and call commond, no indel variance were genearte?

Question

[lemon]

I got my sequence data, and I want to call its snp and indel when reference genome exists. The command 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?

[shubhra.bhattacharya]

Try running it without the LowQual filter?

[finswimmer]

Hello lemon ,

how have you checked that there are no indels in your vcf?

Visualize your bam file with e.g. igv to find a region where a clear insdel is. Retry the variant calling for only this region.

fin swimmer

[lemon]

thanks , when i try to use IGV, i met the same problem that indel were thought to be many snps as you can see in the following picture. it seems that actually a ''G'' was inserted

do u know how to deal with this problem? thank you very much.

[finswimmer]

Indeed this looks a bit strange. So the problem here isn't bcftools, because it rely on the alignment information. Which program and command have you used for alignment?

[lemon]

I used this command to make alignment. thanks

[finswimmer]

Hello and thanks for posting it.

I don't know biokanga. I would try bwa mem and see what happens then. If this works, one can go back to biokanga (if you still want/need to use it) and start finding out what's going on there.

fin swimmer