{"id":147,"date":"2023-07-12T15:21:54","date_gmt":"2023-07-12T07:21:54","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=147"},"modified":"2023-07-12T15:21:54","modified_gmt":"2023-07-12T07:21:54","slug":"convert-sequenza-segment-txt-to-gistic-input","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2023\/07\/12\/convert-sequenza-segment-txt-to-gistic-input\/","title":{"rendered":"Convert Sequenza *segment.txt to GISTIC input"},"content":{"rendered":"

\u539f\u6587\u94fe\u63a5<\/a><\/p>\n

Gistic was designed for SNP6 array data. I saw many papers use it for whole exome sequencing data as well.<\/p>\n

Input format for gistic:<\/h3>\n

segment file:<\/h4>\n

(1) Sample (sample name)
\n(2) Chromosome (chromosome number)
\n(3) Start Position (segment start position, in bases)
\n(4) End Position (segment end position, in bases)
\n(5) Num markers (number of markers in segment)
\n(6) Seg.CN (log2() -1 of copy number)<\/p>\n

The conversion should be log2 (logarithm base 2) - 1, so that copy number 2 is 0.
\nEvery segment start and end in the segments file should appear in the markers file, not the other way around.
\nwhen the copy number is 0 (a homozygous deletion of both copies). You can\u2019t do a log2(0)-1, just put a small number e.g. -5<\/p>\n

marker file:<\/h4>\n

https:\/\/groups.google.com\/a\/broadinstitute.org\/forum\/#!searchin\/gistic-forum\/marker$20file\/gistic-forum\/Vq9WWDiy7jU\/BSFg2zmBZ1EJ<\/a>
\n(1) Marker Name
\n(2) Chromosome
\n(3) Marker Position (in bases)
\nNote gistic2 does not require a marker file anymore.<\/p>\n

sequenza gives a segment file. Segmentation was done by copynumber bioconductor package.
\n13 columns of the segments.txt file:
\n"chromosome" "start.pos" "end.pos" "Bf" "N.BAF" "sd.BAF" "depth.ratio" "N.ratio" "sd.ratio" "CNt" "A" "B" "LPP"
\nWe only need the chromosome, start.pos, end.pos, N.BAF and depth.ratio columns.
\nThe depth.ratio column is the GC content normalized ratio. a depth ratio of 1 means it has copy number of 2 (the same as the normal blood control in my case).
\nIt is not log2(2^ depth.ratio) -1 rather log2(2 <\/em> depth.ratio) - 1<\/p>\n

I have a bunch of sgement files in the same folder.
\nadd the sample name in the final column and do the log2 math in R.<\/p>\n

library(tidyverse)\nlibrary(readr)\nseg_files<- list.files(".", pattern = "*segments.txt", full.names = F) \n\nseg_dat_list <- lapply(seg_files, function(f) {\n        dat<- read_tsv(f, col_names = T, col_types = cols(.default = col_character()))\n        sample<- gsub("_vs_.*segments.txt", "", f)\n        dat$sample<- sample\n        return(dat)\n})\n\nseg_dat <- do.call(rbind, seg_dat_list)\n\ngistic_input<- seg_dat %>% select(sample, chromosome, start.pos, end.pos, N.BAF, depth.ratio) %>% mutate(depth.ratio = as.numeric(depth.ratio)) %>% mutate(depth.ratio = log2(2 * depth.ratio) -1)\n\nwrite_tsv(gistic_input, "all_segments.txt")<\/code><\/pre>\n
Back to bash:<\/p>\n
## marker file:\n\ncat all_segments.txt | sed '1d' | cut -f2,3 > markers.txt\ncat all_segments.txt | sed '1d' | cut -f2,4 >> markers.txt\n\n## sort the files by chromosome, take the unique ones and number the markers.\n\ncat markers.txt | sort -V -k1,1 -k2,2nr | uniq | nl > markers_gistic.txt<\/code><\/pre>\n
Run gistic
\nmodify the gistic2 script a bit. e.g. change MCR_ROOT folder path<\/p>\n
#!\/bin\/sh\n## set MCR environment and launch GISTIC executable\n\n## NOTE: change the line below if you have installed the Matlab MCR in an alternative location\nMCR_ROOT=\/scratch\/genomic_med\/apps\/Matlab_Complier_runTime\nMCR_VER=v83\n\necho Setting Matlab MCR root to $MCR_ROOT\n\n## set up environment variables\nLD_LIBRARY_PATH=$MCR_ROOT\/$MCR_VER\/runtime\/glnxa64:$LD_LIBRARY_PATH\nLD_LIBRARY_PATH=$MCR_ROOT\/$MCR_VER\/bin\/glnxa64:$LD_LIBRARY_PATH\nLD_LIBRARY_PATH=$MCR_ROOT\/$MCR_VER\/sys\/os\/glnxa64:$LD_LIBRARY_PATH\nexport LD_LIBRARY_PATH\nXAPPLRESDIR=$MCR_ROOT\/$MCR_VER\/MATLAB_Component_Runtime\/v83\/X11\/app-defaults\nexport XAPPLRESDIR\n\n## launch GISTIC executable\n.\/gp_gistic2_from_seg $@<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
\u539f\u6587\u94fe\u63a5 Gistic was designed for SNP6 array data. I saw man…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-147","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/147","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=147"}],"version-history":[{"count":1,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/147\/revisions"}],"predecessor-version":[{"id":148,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/147\/revisions\/148"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=147"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=147"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=147"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}