getSNP: getSNP - finding SNPs in all samples for regions specified by...
In ampliQueso: Analysis of amplicon enrichment panels
Description
Usage
Arguments
Value
Author(s)
Description
Finding SNPs in all samples for regions specified by a BED file (sequential version) using Samtools mpileup functionality.
Please make sure that samtools executables are installed and available from command line without specifing the full path(e.g. added to the PATH environment variable)
Usage
1
Arguments
covdesc
Covdesc-like data frame - BAM files are read from row names. Similar to covdesc in simpleaffy and rnaSeqMap - tab delimited table of BAM files and groupings. This is the table of experimental design.
minQual
number specifing the minimum quality of the SNPs returned by samtools used to filter out these of poor quality. Please refer to
Samtools documentation for further details on the definition of this measure.
refSeqFile
Reference sequence in FASTA format used for SNPs detection.
bedFile
BED file with same genomic coordinates as in BAMs (preferably standard hg19)
iParallel
boolean specifing whether calculations shoulb be run in parallel,true by default,
The degree of parallelism is set up automagically and by default equals to the number of logical CPU cores.
Value
list of data frames, for one sample each containing coordinates of the SNP with its quality
Author(s)
Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski
ampliQueso documentation built on May 2, 2019, 12:45 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s)
Description
Finding SNPs in all samples for regions specified by a BED file (sequential version) using Samtools mpileup functionality. Please make sure that samtools executables are installed and available from command line without specifing the full path(e.g. added to the PATH environment variable)
Usage
1 |
Arguments
covdesc |
Covdesc-like data frame - BAM files are read from row names. Similar to covdesc in simpleaffy and rnaSeqMap - tab delimited table of BAM files and groupings. This is the table of experimental design. |
minQual |
number specifing the minimum quality of the SNPs returned by samtools used to filter out these of poor quality. Please refer to Samtools documentation for further details on the definition of this measure. |
refSeqFile |
Reference sequence in FASTA format used for SNPs detection. |
bedFile |
BED file with same genomic coordinates as in BAMs (preferably standard hg19) |
iParallel |
boolean specifing whether calculations shoulb be run in parallel,true by default, The degree of parallelism is set up automagically and by default equals to the number of logical CPU cores. |
Value
list of data frames, for one sample each containing coordinates of the SNP with its quality
Author(s)
Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.