Hello I am using bcftools to call variants with this command:
bcftools mpileup -Ou -b bamlist -f ref.fasta | bcftools call -Ob -mv >variant.bcf
However, for some specific variants that I know to exist (looking at bam files with IGV), I do not get variant calls. The read depth is shallow 3-4 reads per site. How do I force bcftools to output all possible variants, even tough they have low probability?
There are some default parameters set like p-value < 0.5 and potentially others. Try setting these to higher values.
bcftools call -h
Another alternative is to not put the -v there at all, that way you'll get the genotype likelihoods for all positions (potentially a huge file)
I was trying to use the p-value > 0.5 option which is available only under the -c option, but it did not solve the problem.
I have added the FORMAT/AD and DP to the output, omitted the -v flag and added bcftools filter to the pipe and got the desired result. I can further look at the AD (allele depth) to decide which SNP is true.
bcftools mpileup -a FORMAT/AD,FORMAT/DP -Ou -b bamlist -f ref.fasta | bcftools call -Ou -m | bcftools filter -Ob -i 'F_MISSING<0.1&&MAF>0.1' >variant.bcf
thanks for sharing the solution.
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Hi,
I have the same problem and i would also like to force call bcftools in order to get all the variants of my bam. also i am aware of some variants (examining the bam files with Tablet) but they are not called
I am using this command
I tried to apply the command you shared but it creates a file that I can't read. How can I do it? Do you have any suggestions?
tks for the help
Stefania
You should start relaxing the filters (if it was not apparent from the comment I added in other post you created). You are filtering things with
-q and -Qoptions.