I am a beginner in variant calling with
samtools and trying to understand its usage. Often the options
-F are used, together with the option
-p. This is what appears in the documentation for
-p, --per-sample-mF apply -m and -F per-sample for increased sensitivity -m, --min-ireads INT minimum number gapped reads for indel candidates  -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:
-Fapply 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
500reads overlapping a genomic region at least
0.002*500=1reads should be gapped in order to do indel related calculations?
-mis TRUE and
-Fis 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.