@@ -69,4 +69,4 @@ biocViews: CopyNumberVariation, Software, Sequencing,

     VariantAnnotation, VariantDetection, Coverage, ImmunoOncology

 NeedsCompilation: no

 ByteCompile: yes

-RoxygenNote: 7.2.3

+RoxygenNote: 7.2.3.9000

@@ -17,7 +17,7 @@

 #' which potentially have allelic fractions smaller than 1 due to artifacts or

 #' contamination. If a matched normal is available, this value is ignored,

 #' because homozygosity can be confirmed in the normal.

-#' @param contamination.range Count variants in dbSNP with allelic fraction

+#' @param contamination.range Count variants in germline databases with allelic fraction

 #' in the specified range. If the number of these putative contamination

 #' variants exceeds an expected value and if they are found on almost all

 #' chromosomes, the sample is flagged as potentially contaminated and extra

@@ -49,7 +49,7 @@

 #' the specified size in bp. Requires \code{target.granges}.

 #' @param DB.info.flag Flag in INFO of VCF that marks presence in common

 #' germline databases. Defaults to \code{DB} that may contain somatic variants

-#' if it is from an unfiltered dbSNP VCF.

+#' if it is from an unfiltered germline database.

 #' @return A list with elements \item{vcf}{The filtered \code{CollapsedVCF}

 #' object.} \item{flag}{A flag (\code{logical(1)}) if problems were

 #' identified.} \item{flag_comment}{A comment describing the flagging.}

@@ -160,7 +160,7 @@ interval.padding = 50, DB.info.flag = "DB") {

             ifelse(fractionContaminated > minFractionContaminated, "maybe", "unlikely"))

     }

-    # do we have many low allelic fraction calls that are in dbSNP on basically

+    # do we have many low allelic fraction calls that are in germline databases on basically

     # all chromosomes? then we found some contamination

     if (sum(runLength(seqnames(rowRanges(vcf[idx]))) > 3) >= 20 &&

         fractionContaminated >= minFractionContaminated) {

@@ -223,7 +223,7 @@ interval.padding = 50, DB.info.flag = "DB") {

     }

     if (!is.null(info(vcf)[[DB.info.flag]]) &&

         sum(info(vcf)[[DB.info.flag]]) < nrow(vcf) / 2) {

-        flog.warn("Less than half of variants in dbSNP. Make sure that VCF %s",

+        flog.warn("Less than half of variants are likely somatic. Make sure that VCF %s",

             "contains both germline and somatic variants.")

     }

@@ -501,7 +501,7 @@ function(vcf, tumor.id.in.vcf, allowed = 0.05) {

     } else if (!is.null(info(vcf)[[POPAF.info.field]]) &&

         max(unlist(info(vcf)[[POPAF.info.field]]), na.rm = TRUE) > 0.05) {

         if (max(unlist(info(vcf)[[POPAF.info.field]]), na.rm = TRUE) > 1.1) {

-            flog.info("Maximum of POPAP INFO is > 1, assuming -log10 scaled values")

+            flog.info("Maximum of POPAF INFO is > 1, assuming -log10 scaled values")

             db <- info(vcf)[[POPAF.info.field]] < -log10(min.pop.af)

         } else {

             db <- info(vcf)[[POPAF.info.field]] > min.pop.af

@@ -523,7 +523,7 @@ function(vcf, tumor.id.in.vcf, allowed = 0.05) {

     newInfo <- DataFrame(

         Number = 0,

         Type = "Flag",

-        Description = "dbSNP Membership",

+        Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or dbSNP membership",

         row.names = DB.info.flag)

     info(header(vcf)) <- rbind(info(header(vcf)), newInfo)

     info(vcf)[[DB.info.flag]] <- db

@@ -170,7 +170,7 @@ ss) {

 .getAFPlotGroups <- function(r, single.mode) {

     if (single.mode) {

-        groupLevels <- c("dbSNP/germline", "dbSNP/somatic", "novel/somatic",

+        groupLevels <- c("dbSNP or POPAF/germline", "dbSNP or POPAF/somatic", "novel/somatic",

             "novel/germline", "COSMIC/germline", "COSMIC/somatic", "contamination")

         r$group <- groupLevels[1]

         r$group[r$prior.somatic < 0.1 & r$ML.SOMATIC] <- groupLevels[2]

@@ -566,7 +566,7 @@ ss) {

                 y=r$ML.AR[r$ML.SOMATIC][idx.labels],

                 labels=scatter.labels[idx.labels])

         }

-        idxSomatic <- !grepl("germline|dbSNP|contamination", as.character(r$group))

+        idxSomatic <- !grepl("germline|dbSNP or POPAF|contamination", as.character(r$group))

         if (sum(idxSomatic)) {

             colSomatic <- mycol.palette$color[match(names(sort(table(r$group[idxSomatic]),

                 decreasing=TRUE)[1]), mycol.palette$group)]

@@ -80,7 +80,7 @@ readAllelicCountsFile <- function(file, format, zero=NULL) {

     info(header(vcf)) <- DataFrame(

         Number = "0",

         Type = "Flag",

-        Description = "dbSNP Membership",

+        Description = "Likely somatic status, based on SOMATIC or Cosmic.CNT info fields, population allele frequency, or dbSNP membership",

         row.names = "DB")

     geno(header(vcf)) <- DataFrame(

@@ -3,10 +3,10 @@

 #' This function takes as input tumor and normal control coverage data and

 #' a VCF containing allelic fractions of germline variants and somatic

 #' mutations. Normal control does not need to be from the same patient.

-#' In case VCF does not contain somatic status, it should contain dbSNP and

-#' optionally COSMIC annotation. Returns purity and ploidy combinations,

-#' sorted by likelihood score. Provides copy number and LOH data, by both

-#' gene and genomic region.

+#' In case VCF does not contain somatic status, it should contain either

+#' dbSNP or population allele frequencies, and  optionally COSMIC annotation.

+#' Returns purity and ploidy combinations, sorted by likelihood score.

+#' Provides copy number and LOH data, by both gene and genomic region.

 #'

 #'

 #' @param normal.coverage.file Coverage file of normal control (optional

@@ -29,7 +29,7 @@

 #' @param vcf.file VCF file.

 #' Optional, but typically needed to select between local optima of similar

 #' likelihood. Can also be a \code{CollapsedVCF}, read with the \code{readVcf}

-#' function.  Requires a DB info flag for dbSNP membership. The default

+#' function.  Requires a DB info flag for likely somatic status. The default

 #' \code{fun.setPriorVcf} function will also look for a Cosmic.CNT slot (see

 #' \code{cosmic.vcf.file}), containing the hits in the COSMIC database. Again,

 #' do not expect very useful results without a VCF file.

@@ -131,10 +131,10 @@

 #' likelihood score calculation. Note that bias is reported on an inverse

 #' scale; a variant with mapping bias of 1 has no bias.

 #' @param max.pon Exclude variants found more than \code{max.pon} times in

-#' pool of normals and not in dbSNP. Requires \code{mapping.bias.file} in

-#' \code{\link{setMappingBiasVcf}}. Should be set to a value high enough

+#' pool of normals and not in germline databases. Requires \code{mapping.bias.file}

+#' in \code{\link{setMappingBiasVcf}}. Should be set to a value high enough

 #' to be much more likely an artifact and not a true germline variant not

-#' present in dbSNP.

+#' present in germline databases.

 #' @param min.variants.segment Flag segments with fewer variants. The

 #' minor copy number estimation is not reliable with insufficient variants.

 #' @param iterations Maximum number of iterations in the Simulated Annealing

@@ -189,7 +189,7 @@

 #' and indexed with bgzip and tabix, respectively.

 #' @param DB.info.flag Flag in INFO of VCF that marks presence in common

 #' germline databases. Defaults to \code{DB} that may contain somatic variants

-#' if it is from an unfiltered dbSNP VCF.

+#' if it is from an unfiltered germline database.

 #' @param POPAF.info.field As alternative to a flag, use an info field that

 #' contains population allele frequencies. The \code{DB} info flag has priority

 #' over this field when both exist.

@@ -8,21 +8,22 @@

 #' function from the VariantAnnotation package.

 #' @param prior.somatic Prior probabilities for somatic mutations. First value

 #' is for the case when no matched normals are available and the variant is not

-#' in dbSNP (second value). Third value is for variants with MuTect somatic

-#' call. Different from 1, because somatic mutations in segments of copy number

-#' 0 have 0 probability and artifacts can thus have dramatic influence on

+#' in germline databases (second value). Third value is for variants with MuTect

+#' somatic call. Different from 1, because somatic mutations in segments of copy

+#' number 0 have 0 probability and artifacts can thus have dramatic influence on

 #' likelihood score. Forth value is for variants not labeled as somatic by

 #' MuTect. Last two values are optional, if vcf contains a flag Cosmic.CNT, it

-#' will set the prior probability for variants with CNT > 2 to the first of

+#' will set the prior probability for variants with CNT > 6 to the first of

 #' those values in case of no matched normal available (0.995 default).  Final

-#' value is for the case that variant is in both dbSNP and COSMIC > 2.

+#' value is for the case that variant is in both germline databases and

+#' COSMIC count > 6.

 #' @param tumor.id.in.vcf Id of tumor in case multiple samples are stored in

 #' VCF.

 #' @param min.cosmic.cnt Minimum number of hits in the COSMIC database to 

 #' call variant as likely somatic.

 #' @param DB.info.flag Flag in INFO of VCF that marks presence in common

 #' germline databases. Defaults to \code{DB} that may contain somatic variants

-#' if it is from an unfiltered dbSNP VCF.

+#' if it is from an unfiltered germline database.

 #' @param Cosmic.CNT.info.field Info field containing hits in the Cosmic database

 #' @return The \code{vcf} with \code{numeric(nrow(vcf))} vector with the

 #' prior probability of somatic status for each variant in the 

@@ -59,14 +60,14 @@ setPriorVcf <- function(vcf, prior.somatic = c(0.5, 0.0005, 0.999, 0.0001,

          if (!is.null(info(vcf)[[Cosmic.CNT.info.field]])) {

              flog.info("Found COSMIC annotation in VCF. Requiring %i hits.", 

                 min.cosmic.cnt)

-             flog.info("Setting somatic prior probabilities for hits to %f or to %f if in both COSMIC and dbSNP.", 

+             flog.info("Setting somatic prior probabilities for hits to %f or to %f if in both COSMIC and likely somatic based on dbSNP membership or population allele frequency.", 

                 tmp[5], tmp[6])

              prior.somatic[which(info(vcf)[[Cosmic.CNT.info.field]] >= min.cosmic.cnt)] <- tmp[5]

              prior.somatic[which(info(vcf)[[Cosmic.CNT.info.field]] >= min.cosmic.cnt & 

                 info(vcf)[[DB.info.flag]])] <- tmp[6]

          } else {

-             flog.info("Setting somatic prior probabilities for dbSNP hits to %f or to %f otherwise.", 

+             flog.info("Setting somatic prior probabilities for likely somatic hits to %f or to %f otherwise.", 

                 tmp[2], tmp[1])

          }      

     }     

@@ -102,7 +102,7 @@ option_list <- list(

         help = "Maximum considered ploidy [default %default]"),

     make_option(c("--max-copy-number"), action = "store", type = "double",

         default =  max(eval(formals(PureCN::runAbsoluteCN)$test.num.copy)),

-        help = "Maximum allele-specific integer copy number [default %default]"),

+        help = "Maximum allele-specific integer copy number, only used for fitting allele-specific copy numbers. Higher copy numbers might still be inferred and reported [default %default]"),

     make_option(c("--post-optimize"), action = "store_true", default = FALSE,

         help = "Post-optimization [default %default]"),

     make_option(c("--bootstrap-n"), action = "store", type = "integer", default = 0,

@@ -44,7 +44,7 @@ which potentially have allelic fractions smaller than 1 due to artifacts or

 contamination. If a matched normal is available, this value is ignored,

 because homozygosity can be confirmed in the normal.}

-\item{contamination.range}{Count variants in dbSNP with allelic fraction

+\item{contamination.range}{Count variants in germline databases with allelic fraction

 in the specified range. If the number of these putative contamination

 variants exceeds an expected value and if they are found on almost all

 chromosomes, the sample is flagged as potentially contaminated and extra

@@ -87,7 +87,7 @@ the specified size in bp. Requires \code{target.granges}.}

 \item{DB.info.flag}{Flag in INFO of VCF that marks presence in common

 germline databases. Defaults to \code{DB} that may contain somatic variants

-if it is from an unfiltered dbSNP VCF.}

+if it is from an unfiltered germline database.}

 }

 \value{

 A list with elements \item{vcf}{The filtered \code{CollapsedVCF}

@@ -98,7 +98,7 @@ deviation, used to model likelihood of sub-clonal copy number events.}

 \item{vcf.file}{VCF file.

 Optional, but typically needed to select between local optima of similar

 likelihood. Can also be a \code{CollapsedVCF}, read with the \code{readVcf}

-function.  Requires a DB info flag for dbSNP membership. The default

+function.  Requires a DB info flag for likely somatic status. The default

 \code{fun.setPriorVcf} function will also look for a Cosmic.CNT slot (see

 \code{cosmic.vcf.file}), containing the hits in the COSMIC database. Again,

 do not expect very useful results without a VCF file.}

@@ -233,10 +233,10 @@ likelihood score calculation. Note that bias is reported on an inverse

 scale; a variant with mapping bias of 1 has no bias.}

 \item{max.pon}{Exclude variants found more than \code{max.pon} times in

-pool of normals and not in dbSNP. Requires \code{mapping.bias.file} in

-\code{\link{setMappingBiasVcf}}. Should be set to a value high enough

+pool of normals and not in germline databases. Requires \code{mapping.bias.file}

+in \code{\link{setMappingBiasVcf}}. Should be set to a value high enough

 to be much more likely an artifact and not a true germline variant not

-present in dbSNP.}

+present in germline databases.}

 \item{iterations}{Maximum number of iterations in the Simulated Annealing

 copy number fit optimization. Note that this an integer optimization problem

@@ -308,7 +308,7 @@ and indexed with bgzip and tabix, respectively.}

 \item{DB.info.flag}{Flag in INFO of VCF that marks presence in common

 germline databases. Defaults to \code{DB} that may contain somatic variants

-if it is from an unfiltered dbSNP VCF.}

+if it is from an unfiltered germline database.}

 \item{POPAF.info.field}{As alternative to a flag, use an info field that

 contains population allele frequencies. The \code{DB} info flag has priority

@@ -354,10 +354,10 @@ input data.}

 This function takes as input tumor and normal control coverage data and

 a VCF containing allelic fractions of germline variants and somatic

 mutations. Normal control does not need to be from the same patient.

-In case VCF does not contain somatic status, it should contain dbSNP and

-optionally COSMIC annotation. Returns purity and ploidy combinations,

-sorted by likelihood score. Provides copy number and LOH data, by both

-gene and genomic region.

+In case VCF does not contain somatic status, it should contain either

+dbSNP or population allele frequencies, and  optionally COSMIC annotation.

+Returns purity and ploidy combinations, sorted by likelihood score.

+Provides copy number and LOH data, by both gene and genomic region.

 }

 \examples{

@@ -19,14 +19,15 @@ function from the VariantAnnotation package.}

 \item{prior.somatic}{Prior probabilities for somatic mutations. First value

 is for the case when no matched normals are available and the variant is not

-in dbSNP (second value). Third value is for variants with MuTect somatic

-call. Different from 1, because somatic mutations in segments of copy number

-0 have 0 probability and artifacts can thus have dramatic influence on

+in germline databases (second value). Third value is for variants with MuTect

+somatic call. Different from 1, because somatic mutations in segments of copy

+number 0 have 0 probability and artifacts can thus have dramatic influence on

 likelihood score. Forth value is for variants not labeled as somatic by

 MuTect. Last two values are optional, if vcf contains a flag Cosmic.CNT, it

-will set the prior probability for variants with CNT > 2 to the first of

+will set the prior probability for variants with CNT > 6 to the first of

 those values in case of no matched normal available (0.995 default).  Final

-value is for the case that variant is in both dbSNP and COSMIC > 2.}

+value is for the case that variant is in both germline databases and

+COSMIC count > 6.}

 \item{tumor.id.in.vcf}{Id of tumor in case multiple samples are stored in

 VCF.}

@@ -36,7 +37,7 @@ call variant as likely somatic.}

 \item{DB.info.flag}{Flag in INFO of VCF that marks presence in common

 germline databases. Defaults to \code{DB} that may contain somatic variants

-if it is from an unfiltered dbSNP VCF.}

+if it is from an unfiltered germline database.}

 \item{Cosmic.CNT.info.field}{Info field containing hits in the Cosmic database}

 }

@@ -947,7 +947,7 @@ NOISY SEGMENTATION & More than \Rcode{max.segments} \\

 NON-ABERRANT & $\geq 99 $\% of genome has identical copy number and $\geq 0.5$\% has second most common state \\

 POLYGENOMIC & $\geq 0.75 \times$ \Rcode{max.non.clonal} fraction of the genome in sub-clonal state \\

 POOR GOF & GoF $<$ \Rcode{min.gof} \\

-POTENTIAL SAMPLE CONTAMINATION & Significant portion of dbSNP variants potentially cross-contaminated \\

+POTENTIAL SAMPLE CONTAMINATION & Significant portion of variants present in germline databases are potentially cross-contaminated \\

 RARE KARYOTYPE & Ploidy $< 1.5$ or  $> 4.5$  \\

 \bottomrule

 \end{tabular}

@@ -1115,12 +1115,12 @@ If a matched normal is not available, it is also helpful to provide

 \Rcode{cosmic.vcf.file} (or via a \Rcode{Cosmic.CNT} INFO field in the VCF).

 While this has limited effect on purity and ploidy estimation due the sparsity

 of hotspot mutations, it often helps in the manual curation to compare how well

-high confidence germline (dbSNP) vs. somatic (COSMIC) variants fit a particular

-purity/ploidy combination. 

+high confidence germline (based on dbSNP membership or POPAF) vs. somatic (COSMIC)

+variants fit a particular purity/ploidy combination. 

 For variant classification (Section~\ref{predictsomatic}), providing COSMIC

-annotation also avoids that hotspot mutations with dbSNP id get assigned a very

-low prior probability of being somatic.

+annotation also avoids that hotspot mutations in germline databases get assigned

+a very low prior probability of being somatic.

 \subsection{ExAC and gnomAD annotation}