| Name : polymutt
| |
| Version : 0.18
| Vendor : obs://build_opensuse_org/home:peralta_jm
|
| Release : 1.1
| Date : 2014-08-09 00:06:32
|
| Group : Scientific/Bioinformatics
| Source RPM : polymutt-0.18-1.1.src.rpm
|
| Size : 87.46 MB
| |
| Packager : (none)
| |
| Summary : A likelihood-based framework for SNVs and de novo mutation calling in families
|
Description :
The program polymutt implemented a likelihood-based framework for
calling single nucleotide variants and detecting de novo point
mutation events in families for next-generation sequencing data.
The program takes as input genotype likelihood format (GLF) files
which can be generated following the Creation of GLF files
instruction and outputs the result in the [VCF] format.
Alternatively polymutt can also take the VCF format input in which
either the PL or the GL field are present. Commonly used variant
calling algorithms such as GATK and samtools by default generate
PL values in the VCF files. Current version works only on biallelic
variants and non-biallelic variants in the VCF files will be ignored.
The variant calling and de novo mutation detection are modeled
jointly within families and can handle both nuclear and extended
pedigrees without consanguinity loops.
Since unrelated individuals are kind of special case of families,
unrelated individuals or a mixture of related and unrelated
individuals can be handled. The relationship is specified in the
input .ped file and for unrelated individuals each of them can be
assigned a unique family ID.
The evidence of variants and de novo mutations are assessed
probabilistically. For a variant, the QUAL value is calculated as
-10*log10(1-posterior(Variant | Data)) and for de novo mutation
events a de novo quality (DQ) value is defined as
log10(lk_denovo / lk_no_denovo) where lk_denovo and lk_no_denovo
are the likelihoods of data allowing and disallowing de novo
mutations respectively. Similarly, for each genotype, a genotype
quality (GQ) value is defined as
-10*log10(1-posterior(Genotype | Data)).
If some individuals in a family are not sequenced, this can be
handled by setting the corresponding GLF file indices to zero
for those family members who are not sequenced, if the input are
GLF files. For VCF input, all individuals in the .ped file but
not in the VCF files are considered missing data (not sequenced).
Variant calling for X, Y and MT has been only lightly tested.
Any comments/suggestions about polymutt and non-autosomal
variant calling in particular are appreciated.
|
RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/home:/peralta_jm:/bioinformatics/openSUSE_13.1/x86_64 |
Hmm ... It's impossible ;-) This RPM doesn't exist on any FTP server
Provides :
polymutt
polymutt(x86-64)
Requires :
