Question: How can I see the low frequency SNP
gravatar for apl00028
15 months ago by
apl0002870 wrote:

I have created a vcf file from bam file using bcftools:

 bcftools mpileup \
--redo-BAQ \
--min-BQ 30 \
--per-sample-mF \
 --annotate \
FORMAT/AD,FORMAT/DP,INFO/AD -f cmv3 scaffold_nofilt_PV002.bam | \
bcftools call --multiallelic-caller --variants-only -Ov > \

After that I visualized this file using R, but It had lower number of records in comparation to IGV program results using the same bam file. I think that it is due to bcftools take only SNP with high frequency.

What modification should do add to the bcftools program to see all records although they have a low frequency?

snp ngs • 336 views
ADD COMMENTlink written 15 months ago by apl0002870


how low is "low"?

fin swimmer

ADD REPLYlink written 15 months ago by finswimmer13k

With a Coveage allele-fraction threshold of 0.05. I see them when I run IGV but I can not with the vcf file:

ADD REPLYlink written 15 months ago by apl0002870
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 890 users visited in the last hour