Dinucleodite variants are marked at single nucleotide variant in BCFTOOLS CALL

Question

[Hans]

Hello I have generated a vcf file using bcftools pileup and bctools call using this code: bcftools mpileup -Ou -f ref.fa in.bam | \ bcftools call -mv -Ov -P 0.5 -o out.vcf Comparing the bam file and the vcf file with IGV I see in some places that in the bam file there are di or trinucleotide variants while in the vcf file I see only snv. Any ideas on how to fix it/or why the vcf ouput is correct? Thank you

[Kevin Blighe]

Can you please paste the complete entries for some of these from the VCF?

[Hans]

 chr2B   26348956        .       T       A       107     .       DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60    GT:PL   1/1:110,6,0

chr3A   545888578       .       A       T       70      .       DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=40    GT:PL   1/1:73,6,0

chr3B   59046285        .       G       A       43.9905 .       DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=26    GT:PL   1/1:47,6,0

[Kevin Blighe]

The DP values indicate that depth of coverage over the position is low. Have you rigorously checked the reads covering this region in IGV to gauge their quality? Keep in mind that NGS data is inherently noisy.

[Hans]

I did not mention it, but it is not an alignment of reads but gene sequences from assembly of one species against the reference of a sister species.