How do I call all the variants with BCFTOOLS?
Hello
I am using bcftools to call variants with this command:
bcftools mpileup -B -q30 -Q30 -f reference.fasta -a FORMAT/DP,FORMAT/AD --threads 6 -R list_of_specific_position.txt file.bam | bcftools call -m -f GQ -O v -o call_variant.vcf
For some specific variants that I am aware of (examining the bam files with Tablet), I do not get variant calls. The depth, for some, is 6 reads per site and yet they are not being called. How can I force bcftools to produce all possible variants, even if they have a low probability?
Thanks for the help
Stefania
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