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Adjusting Allele Frequency when calling variants with bcftools
Hi all,
I'm currently using bcftools to call variants from NGS data. In my case the allele frequency of the variants is not always 50 or 100%, but can also be quite low (below 10%). However, the coverage is generally quite good.
I noticed that I missed quite a few variants because of low allele frequency even though they were supported by many high quality alignments.
Is it somehow possible to adjust bcftools for these cases by lowering the impact of the allele frequency when assessing the quality of a variant call? Right now these variants are not in the variant output of BCF tools at all.
Thx for your time,
Sebastian
I'm currently using bcftools to call variants from NGS data. In my case the allele frequency of the variants is not always 50 or 100%, but can also be quite low (below 10%). However, the coverage is generally quite good.
I noticed that I missed quite a few variants because of low allele frequency even though they were supported by many high quality alignments.
Is it somehow possible to adjust bcftools for these cases by lowering the impact of the allele frequency when assessing the quality of a variant call? Right now these variants are not in the variant output of BCF tools at all.
Thx for your time,
Sebastian