platypusFilter.Rd
This function executes platypusFilter filtering the single_variants.vcf generated by platypys function.
platypusFilter( group = c("sudo", "docker"), data.folder = getwd(), scratch.folder, GQ, minSampGQ, NR, minSampNR, NV, minSampNV, normal_samples, GT_normal, minSampGT_normal, tumoral_samples, GT_tumoral, minSampGT_tumoral, stringent_filter, annotation )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
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 |
if (FALSE) { #filtering platypus results platypusFilter(group="docker", data.folder="/archive/home/rcaloger/data/platypus_tests/mm10ENSEMBL", scratch.folder="/scratch/users/rcaloger/", 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") }