Question: Dinucleodite variants are marked at single nucleotide variant in BCFTOOLS CALL
0
gravatar for Hans
7 months ago by
Hans70
Hans70 wrote:

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

bcftools variant calling • 226 views
ADD COMMENTlink written 7 months ago by Hans70

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

ADD REPLYlink written 7 months ago by Kevin Blighe71k
 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
ADD REPLYlink modified 7 months ago by Kevin Blighe71k • written 7 months ago by Hans70

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by Kevin Blighe71k

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.

ADD REPLYlink written 7 months ago by Hans70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2132 users visited in the last hour
_