platypus: Platypus analysis NOT READY TO GO ON STABLE missing test set

View source: R/platypus.R

platypusR Documentation

Platypus analysis NOT READY TO GO ON STABLE missing test set

Description

This function executes Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data. Platypus requires as input bam and bai files. In case vcf.gz and vcf.idx files are located in the bam folder platypus will use only those positions for SNV calling

Usage

platypus(
  group = c("sudo", "docker"),
  data.folder = getwd(),
  scratch.folder,
  pathRef,
  nameRef,
  threads,
  GQ,
  minSampGQ,
  NR,
  minSampNR,
  NV,
  minSampNV,
  normal_samples,
  GT_normal,
  minSampGT_normal,
  tumoral_samples,
  GT_tumoral,
  minSampGT_tumoral,
  stringent_filter = 0,
  annotation = c("hg19", "mm10")
)

Arguments

group

a character string. Two options: sudo or docker, depending to which group the user belongs

data.folder

a character string indicating the folder where bams and vcf files are located and where output will be written

scratch.folder

a character string indicating the path of the scratch folder

pathRef

Path of the foldert that contains the fasta file of the genome

nameRef

name of the fasta file inside pathRef, the fastq has to be indexed with samtools faidx

threads

a number indicating the number of cores to be used from the application

GQ

min GQ value to consider (extreme included)

minSampGQ

min number of samples with GQ value (extreme included), usually we start with 85% of the samples

NR

min NR value to consider (extreme included), the number of reads covering the SNV region

minSampNR

min number of samples with NR value (extreme included), usually we start with 85% of the samples

NV

min NV value to consider (extreme included), the n of reads with the SNV

minSampNV

min number of samples with NV value (extreme included)

normal_samples

string with names (group names of bam files) of normal samples separated by hash, write NULL if you do not want to use GT filter in normal samples

GT_normal

GT value in normal samples to consider, type "NO" if you do not want to use this filter, else e.g. you might use 0/0

minSampGT_normal

min number of normal samples with GT value

tumoral_samples

string with names (group names of bam files) of tumoral samples separated by &, write NULL if you do not want to use GT filter in normal samples

GT_tumoral

GT value in tumoral samples to consider, type "NO" if you do not want to use this filter. Type e.g. 0/0 if you do not want to consider this genotype.

minSampGT_tumoral

min number of tumoral samples in which the GT value is NOT present

stringent_filter

To enable the filter (it keeps only the variants with "PASS" value or the variants that have only the "alleleBias" value) use 1 or 0 to disable it

annotation

hg19 and mm10 are actually available for the annotation of the detected SNVs

Author(s)

Riccardo Panero, riccardo.panero[at]gmail[dot]com, Bioinformatics and Genomics unit, University of Torino Italy

Examples

## Not run: 
    #running platypus with some threshold provided by sottoriva analysis
 platypus(group="docker", data.folder="/archive/home/rcaloger/data/platypus_tests/hg19UCSC", 
        scratch.folder="/scratch/users/rcaloger/", pathRef="/archive/home/rcaloger/hg19_exome", 
        nameRef="hg19_clean.fasta", threads=96, GQ=10, minSampGQ=2, NR=10, minSampNR=2, NV=3, 
        minSampNV=1, normal_samples="475blood", GT_normal="0/0", 
        minSampGT_normal=1, tumoral_samples="1864p1#1864p22", GT_tumoral="0/0", 
        minSampGT_tumoral=1, stringent_filter=0, annotation="hg19")
 platypus(group="docker", data.folder="/archive/home/rcaloger/data/platypus_tests/hg19ENSEMBL", 
        scratch.folder="/scratch/users/rcaloger/", pathRef="/archive/home/rcaloger/hg19star", 
        nameRef="genome.fa", threads=96,GQ=10, minSampGQ=2, NR=10, minSampNR=2, NV=3, 
        minSampNV=1, normal_samples="5275001-HS", GT_normal="0/0", 
        minSampGT_normal=1, tumoral_samples="5275001-LSG1#5275001-LSGIII", 
        GT_tumoral="0/0", minSampGT_tumoral=1, stringent_filter=0, annotation="hg19")
 platypus(group="docker", data.folder="/archive/home/rcaloger/data/platypus_tests/mm10ENSEMBL", 
        scratch.folder="/scratch/users/rcaloger/", pathRef="/archive/home/rcaloger/mm10star", 
        nameRef="genome.fa", threads=96, GQ=10, minSampGQ=2, NR=10, minSampNR=2, NV=3, 
        minSampNV=1, normal_samples="MAMBO43", GT_normal="0/0", 
        minSampGT_normal=1, tumoral_samples="MAMBO43TRT#MAMBO43TRNT", GT_tumoral="0/0", 
        minSampGT_tumoral=1, stringent_filter=0, annotation="mm10")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.