Entering edit mode
3.7 years ago
gwyneth0011
•
0
I tried to use Bcftools to calculate allele frequency by SNP variants after bowtie 2 alignment.
bcftools mpilup --redo-BAQ --min-BQ 30 --per-sample-mF --annotate FORMAT/AD, FORMAT/ADF, FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR -F reference.faa.txt reads-sorted.bam } bcftools call --multiallelic-caller --variants0only -0v > new.vcf
And after +fill-tags for AF, I used query to calculate AF for me. However, all position show AF: 0.5? I am confused how to calculate SNP allele frequency estimation in DNA pools.
