I have been carrying out variant calling after alignment using bcftools and extracting a consensus fasta file for small viral genomes for downstream analysis using
bcftools consensus -f ref.fa test.vcf > consensus.fa
I want more control over the variant calling parameters but can't figure out a way to do this using bcftools call from the manual. I have found that VarScan offers more options for minimum coverage, minimum reads, minimum quality etc... but I then can't find a way to extract a consensus fasta file from the output file.
I have two questions
- Please could anyone help me to extract a consensus fasta file from a VarScan pileup2cns output
- Please could anyone help me to find out how I can set parameters such as minimum variant coverage, minimum variant frequency using the bcftools call function?