Hello all.
I have a need to call variants for specific genes when I expect the fraction of reads having the alternate base to be very low, possibly in the range of 5% or lower. Examples of where this might be useful are to detect mutations present in a small fraction of cancer cells, or in any other tissues that are mosaic for the mutation.
I have tried to change the parameters of samtools to be as lenient as possible, but I have variants that it will not call (I use -B, I adjust -d, I've tried all the bcftools options). I have also tried GATK with the most lenient settings possible and can't get it to output such variants.
Do you have suggestions for a variant caller that can do what I want? Basically I want to get every position that has at least 3 alternate reads, regardless of the number of reference reads. I may just roll my own caller by going through the old samtools pileup output, but it will probably be super inefficient. Any advice?
I have a need to call variants for specific genes when I expect the fraction of reads having the alternate base to be very low, possibly in the range of 5% or lower. Examples of where this might be useful are to detect mutations present in a small fraction of cancer cells, or in any other tissues that are mosaic for the mutation.
I have tried to change the parameters of samtools to be as lenient as possible, but I have variants that it will not call (I use -B, I adjust -d, I've tried all the bcftools options). I have also tried GATK with the most lenient settings possible and can't get it to output such variants.
Do you have suggestions for a variant caller that can do what I want? Basically I want to get every position that has at least 3 alternate reads, regardless of the number of reference reads. I may just roll my own caller by going through the old samtools pileup output, but it will probably be super inefficient. Any advice?
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