Samtools Mpileup And Bcftools Parameter

Question

[Ashutosh Pandey]

Hi,

I am currently using new samtools 0.1.17. In older versions of samtools there was a -r parameter explained below:

-r FLOAT  prior of a difference between two haplotypes (for -c) [0.001]

As I work with inbred mice sample I used to use -r .0001 (less heterozygosity than default) with the older version of samtools to call SNPs and Indels.

I can't see the same parameter in new version of samtools. Do we have some similar parameter in the new samtools ?

I found a parameter in bcftools view function:

-t FLOAT    Scaled muttion rate for variant calling [0.001] . Is it same as the one discussed above ?
OR

the new variant calling algorithm in samtools doesn't care about the old -r parameter now ?

Thanks,

Answer 1

[Istvan Albert]

The reason for this most likely is to better separate the two steps that in the past may have been used concurrently.

Samtools collects summary information in the input BAMs, computes the likelihood of data given each possible genotype and stores the likelihoods in the BCF format (see below). It does not call variants. Bcftools applies the prior and does the actual calling.

http://samtools.sourceforge.net/mpileup.shtml

[Ashutosh Pandey]

Hey Istvan,

Thanks for the explanation above. I understood that the new "samtools" has divided the variant calling into two parts: Genotype likelihood calculation and then filtering based on users criteria. I am sure that you have already given me the answer above but can you be more straightforward whether I can use the -t parameter as as a substitute of -r parameter. In other words, if I want to call for variants in inbred mice strain where heterozygosity < .0001 , should i use -t .0001 (scaled mutation rate for variant calling [default 0.001]).

Thanks.

[Istvan Albert]

well the fact that -r has been removed says to me that the two were identical in their meaning but that the latter -t usage is preferred.