Hello,

I am a beginner in variant calling with samtools and trying to understand its usage. Often the options -m and -F are used, together with the option -p. This is what appears in the documentation for samtools mpileup:

  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity
  -m, --min-ireads INT    minimum number gapped reads for indel candidates [1]
  -F, --gap-frac FLOAT    minimum fraction of gapped reads [0.002]

-m is explicit and it applies to indel detection, whereas -F deals with gapped reads, which I guess applies to indel detection as well. Also, since -p applies both options per-sample, I would guess that they address the same type of analysis (indel detection).

My questions are:

• Do both -m and -F apply to indel detection and have nothing to do with SNP detection?

• How to interpret the default value of -F. Is it correct to say that out of 500 reads overlapping a genomic region at least 0.002*500=1 reads should be gapped in order to do indel related calculations?

• What if -mis TRUE and -F is not? (i.e. there is 1 gapped read, but 505 reads overlap the region).

• When would I want to modify the default values? It seems that the defaults are very low.

Thanks!