Check the header of Columbia Eigen tab delimited files
Precomputed Eigen scores are available at Download Eigen/Eigen-PC scores.
It’s weird that my tabix -h or tabix -H cannot print the headers of those .bgz files.
Erik:Downloads$ tabix --version
tabix (htslib) 1.3.2-228-g0c32631
Copyright (C) 2017 Genome Research Ltd.
So I need to decompress one such file to inspect. However, my bgzip cannot recognize the .bgz suffix…
Erik:Downloads$ bgzip -d Eigen_hg19_noncoding_annot_chr21.tab.bgz
[bgzip] Eigen_hg19_noncoding_annot_chr21.tab.bgz: unknown suffix -- ignored
A workaround is to change it into a .gz file.
Erik:Downloads$ mv Eigen_hg19_noncoding_annot_chr21.tab.bgz Eigen_hg19_noncoding_annot_chr21.tab.gz
Erik:Downloads$
Erik:Downloads$ bgzip -cd Eigen_hg19_noncoding_annot_chr21.tab.gz | head -n3
chr position ref alt GERP_NR GERP_RS PhyloPri PhyloPla PhyloVer PhastPri PhastPla PhastVer H3K4Me1 H3K4Me3 H3K27ac TFBS_max TFBS_sum TFBS_num OCPval DnaseSig DnasePval FaireSig FairePval PolIISig PolIIPval ctcfSig ctcfPval cmycSig cmycPval Eigen-raw Eigen-phred Eigen-PC-raw Eigen-PC-phred
21 9411194 G A 0 0 0.121 0.119 0.251 0.117 0.053 0.055 1 2.2 1.08 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.343630566947083 0.857783 -0.220709412747219 0.69382
21 9411194 G C 0 0 0.121 0.119 0.251 0.117 0.053 0.055 1 2.2 1.08 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.343630566947083 0.857783 -0.220709412747219 0.69382
There must be some other way to fix the “unknown suffix” issue but I am not interested in so far…
From the output we can see that:
Eigen-rawis the 30th column (counting from 1, hereinafter)Eigen-phredthe 31stEigen-PC-rawthe 32ndEigen-PC-phredthe 33rd
Update: Thanks to Iuliana Ionita-Laza, zcat is a better command. It works directly on .bgz files.
Erik:Downloads$ zcat Eigen_hg19_noncoding_annot_chr21.tab.bgz | head -n1
chr position ref alt GERP_NR GERP_RS PhyloPri PhyloPla PhyloVer PhastPri PhastPla PhastVer H3K4Me1 H3K4Me3 H3K27ac TFBS_max TFBS_sum TFBS_num OCPval DnaseSig DnasePval FaireSig FairePval PolIISig PolIIPval ctcfSig ctcfPval cmycSig cmycPval Eigen-raw Eigen-phred Eigen-PC-raw Eigen-PC-phred
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