Are both samtools mpileup options -m and -F only related to indel detection?
0
0
Entering edit mode
2.6 years ago
serpalma.v ▴ 70

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!

mpileup samtools next-gen alignment SNP • 699 views
ADD COMMENT

Login before adding your answer.

Traffic: 943 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6