How can I see the low frequency SNP

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5.0 years ago

apl00028 ▴ 90

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 > \
PV002_nofilt.vcf

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 • 1.0k views

ADD COMMENT • link 5.0 years ago by apl00028 ▴ 90

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Hello,

how low is "low"?

fin swimmer

ADD REPLY • link 5.0 years ago by finswimmer 16k

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

https://bioinformatics-core-shared-training.github.io/intro-to-IGV/InspectingVariantsInIGV.html

ADD REPLY • link 5.0 years ago by apl00028 ▴ 90

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