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

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

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.