Mercurial > repos > elixir-it > vinyl_score_heatmap
changeset 0:a7aa56155a91 draft default tip
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 17 Sep 2020 09:40:37 +0000 |
| parents | |
| children | |
| files | heatmap.xml test-data/heatmap-test.tabular test-data/heatmap_output.png tool_heat_score.R |
| diffstat | 3 files changed, 1318 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap.xml Thu Sep 17 09:40:37 2020 +0000 @@ -0,0 +1,53 @@ +<tool id="heatmap" name="heatmap" version="1"> + <description>This heatmap provides a simple and rapid way to compare the importance of the different components of the score associated of a set of variants that were scored by VINYL. </description> + <requirements> + <requirement type="package" >r-base</requirement> + </requirements> + <command> <![CDATA[ + Rscript --vanilla $__tool_directory__/tool_heat_score.R + + ####INPUT + $fileI $cutoff + + ###OUTPUT + $ofile + + ]]> + </command> + <inputs> + <param format="tabular,csv" name="fileI" type="data" label="scored_tab_file" help="VINYL Tabular output format file. Affected individuals "/> + <param name="cutoff" value="8" min="1" type="float" label="score_cutoff" help="Cut-Off score used for the identification of potentially pathogenic variants"/> + + </inputs> + <outputs> + <data format="png" name="ofile" label="${tool.name} on ${on_string}: png "/> + </outputs> + <stdio> + <regex match="error" + source="stderr" + level="fatal" + description="Unknown error encountered" /> + </stdio> + <tests> + <test> + <param name="fileI" value="heatmap-test.tabular" ftype="tabular" /> + <param name="cutoff" value="30" ftype="float" /> + <output name="ofile" file="heatmap_output.png" ftype="png" /> + </test> + </tests> + <help> +**What it does** +VINYL is a software designed to assist in variant prioritization in medium-large cohort of patients. The program computes an aggregate score, which is based on an extensive collection of publicly available annotations, in order to identify/prioritize variants that are likely to be pathogenic or have a clinical significance. In order to derive an optimal cut off score for the variants, VINYL uses a strategy based on "survival analysis", where the pathogenicity score distribution of the affected individuals is compared with a matched cohort of unaffected individuals. +To facilitate the usage of the software, VINYL is provided in the form of a public Galaxy instance, based on the Laniakea suite. To ensure the maximum level of security, VINYL uses Encrypted data volumes for the storage of the data. + + + +**Important Usage Note** +This wrapper provides an utility that compares the "features" (i.e the score composition) of a set of variants, scored by VINYL. Ideally this method is best suited to compare a set/ensemble of genetic variants that show a score above a user predefined cut-off, in order to understand which type of the score features evaluated by VINYL were the most important in contributing to the score of each single variants. Clustering is used to display variants that have a similar "scoring composition", that is variants that are associated with similar annotations that display a score above a certain cut-off. +This utility should be used to find "patterns" in variant scored by VINYL in order to understand, which specific component of the VINYL score (functional annotation element), was important for every distinct variant, but also to identify groups of variants that are associated with "equivalent" functional features. +To put it simple this tool should show 1) "Why" a variant passed the score cut off (i.e which single components of the score were important for that variant. 2) Which group of variants were associated with similar features. +A brief discussion on how to read/interpret the output of this tools is also provided in the VINYL manual + </help> + <citations> + </citations> +</tool>
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0 0 0 0 0 0 0 0 -7.28 +chr1 228520973 C G 3 0 18 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 1.715 0 0 -5.565 +chr1 228522483 C T 0 0 3 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228523005 TGGGGGT TGGGGGGT 4 0 10 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228523011 T G 0 0 1 OBSCN 2.6 0 0 19.76 0 0 0 0 0 0 0 0 0 22.36 +chr1 228523448 G A 1 0 2 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr1 228523618 G A 6 0 26 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr1 228524961 C A 3 0 18 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr1 228525008 G A 1 0 15 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 6.13 0 2.21 +chr1 228525627 C A 3 0 18 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr1 228525823 C T 0 0 1 OBSCN 2.6 0 0 19.76 0 0 0 0 0 8.59 3.43 0 0 34.38 +chr1 228526011 C T 2 0 15 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228526619 G A 0 0 2 OBSCN 2.6 0 0 0 0 0 0 1.54 4.58 0 0 0 4.13 12.85 +chr1 228526665 T C 6 0 26 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228526742 CCACACACACACACACACACACACACACACACACACGTCCAT CCACACACACACACACACACACACACACACACACACACACACGTCCAT,CCACACACACACACACACACACACACACACACACGTCCAT,CCACACACACACACACACACACACACACACACGTCCAT,CCACACACACACACACACACACACACACACACACACACGTCCAT,CCACACACACACACACACACACACACACACACACACACACGTCCAT 4 5 26 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228527758 G C 0 0 1 OBSCN 2.6 0 0 19.76 0 0 3.36 1.54 4.58 0 3.43 0 0 35.27 +chr1 228528412 G A 3 0 18 OBSCN 2.6 0 0 -9.88 0 0 0 0 4.58 0 0 0 0 -2.7 +chr1 228528563 C G 6 0 26 OBSCN 2.6 0 0 -9.88 0 0 0 1.54 4.58 0 1.715 0 0 0.554999999999999 +chr1 228529129 C A 0 0 8 OBSCN 2.6 0 0 -9.88 0 0 0 0 4.58 0 0 0 0 -2.7 +chr1 228543800 C T 0 0 8 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228547901 C T 5 0 30 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228548197 G A 0 0 8 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 1.715 0 0 -5.565 +chr1 228550344 G A 0 0 1 OBSCN 2.6 0 0 0 0 0 0 0 0 0 0 0 0 2.6 +chr1 228550426 C T 0 0 8 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 1.715 0 0 -5.565 +chr1 228550429 C T 0 0 4 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 1.715 0 0 -5.565 +chr1 228553245 C T 0 0 1 OBSCN 2.6 0 0 19.76 0 0 0 0 0 0 0 0 0 22.36 +chr1 228556788 C T 8 0 35 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228557681 G A 0 0 1 OBSCN 2.6 0 0 19.76 0 0 3.36 1.54 4.58 0 3.43 0 0 35.27 +chr1 228558892 C T 0 0 8 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 3.43 0 0 -0.490000000000001 +chr1 228558952 T G 0 0 1 OBSCN 2.6 0 0 -9.88 0 0 3.36 1.54 0 0 0 0 0 -2.38 +chr1 228559167 C A 0 0 1 OBSCN 2.6 0 0 19.76 0 0 3.36 0 0 0 0 0 0 25.72 +chr1 228559430 G A 0 0 1 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 1.715 0 0 -2.205 +chr1 228559450 G A 0 0 1 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 1.715 0 0 -2.205 +chr1 228559967 C T 0 0 8 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr1 228559994 C T 13 0 46 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 1.715 6.13 0 3.925 +chr1 228560139 A G 33 0 70 OBSCN 2.6 0 0 -9.88 0 0 3.36 1.54 0 0 0 0 0 -2.38 +chr1 228560426 A C 0 0 1 OBSCN 2.6 0 0 19.76 0 0 3.36 1.54 0 0 3.43 0 0 30.69 +chr1 228560592 A G 0 0 2 OBSCN 2.6 0 0 0 0 0 3.36 0 0 0 0 0 4.13 10.09 +chr1 228560700 T C 24 0 59 OBSCN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr1 228562350 T C 0 0 1 OBSCN 2.6 0 0 -9.88 0 0 3.36 1.54 0 0 0 0 0 -2.38 +chr1 228562438 G A 0 0 1 OBSCN 2.6 0 0 9.88 0 0 3.36 0 0 0 1.715 0 0 17.555 +chr1 228564747 G T 0 0 1 OBSCN 2.6 0 0 0 0 0 0 0 0 0 0 0 0 2.6 +chr1 228564884 G A 0 0 9 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 1.715 0 0 -5.565 +chr1 228565208 C T 0 0 1 OBSCN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 228565209 G A 0 0 1 OBSCN 2.6 0 0 0 0 0 0 0 0 0 3.43 0 0 6.03 +chr1 228566126 G T 1 0 2 OBSCN 2.6 0 0 19.76 0 7.97 0 0 0 0 0 0 4.13 34.46 +chr1 229567660 CGGCGGGGAGC CGGGGGGGGAGC,CGGGCGGGGAGC,CGGGGGGGAGC,CGGCGGGGGAGC 0 2 2 ACTA1 2.6 0 0 0 0 0 0 1.54 0 0 0 0 4.13 8.27 +chr1 229567663 C G 1 0 11 ACTA1 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 12.26 0 5.475 +chr1 229567668 A G 0 0 1 ACTA1 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 0 23.9 +chr1 229568632 A G 3 0 20 ACTA1 2.6 0 -1.045 -9.88 0 0 0 3.08 0 0 0 12.26 0 7.015 +chr1 229568637 C G 3 0 18 ACTA1 2.6 0 -1.045 -9.88 0 0 0 3.08 0 0 0 12.26 0 7.015 +chr1 236849952 C T 1 0 5 ACTN2 2.6 -1.045 -1.045 -9.88 0 0 3.36 1.54 4.58 0 0 0 0 0.109999999999999 +chr1 236882303 T C 37 0 74 ACTN2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 236883421 C T 37 0 74 ACTN2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 236894647 G A 5 0 29 ACTN2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 236899042 G A 0 0 9 ACTN2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 236900554 C T 0 0 6 ACTN2 2.6 0 0 -9.88 0 0 3.36 1.54 0 0 0 0 0 -2.38 +chr1 236902594 C G 24 0 58 ACTN2 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr1 236907966 G A 0 0 4 ACTN2 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr1 236914754 T C 0 0 1 ACTN2 2.6 -2.09 0 0 0 0 0 1.54 0 0 0 0 0 2.05 +chr1 236925844 G A 0 0 13 ACTN2 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 4.58 0 0 0 0 -3.25 +chr1 237527741 G T 0 0 1 RYR2 2.6 0 0 0 0 0 0 0 0 0 0 0 0 2.6 +chr1 237540615 A C 1 0 11 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237551376 T A 10 0 40 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237586384 T C 1 0 10 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237608842 C T 0 0 1 RYR2 2.6 0 0 0 0 0 0 1.54 0 0 0 0 0 4.14 +chr1 237617757 C T 9 0 40 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237619993 G A 0 0 1 RYR2 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 0 23.9 +chr1 237620049 T C 8 0 39 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237632512 T C 0 0 1 RYR2 2.6 0 0 0 0 0 0 0 0 0 0 0 0 2.6 +chr1 237655173 A T 0 0 6 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237656289 C T 0 0 1 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237670107 A G 0 0 1 RYR2 2.6 0 0 9.88 0 0 0 1.54 4.58 0 6.86 0 0 25.46 +chr1 237670140 A G 11 0 43 RYR2 2.6 0 0 -9.88 0 0 0 1.54 4.58 0 0 0 0 -1.16 +chr1 237711797 A G 33 0 69 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237753074 ATTTTTTTTTTCTTCCCA ATTTTTTTTTCTTCCCA 7 0 32 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237765311 TAA TA 0 0 1 RYR2 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 0 23.9 +chr1 237774051 C T 0 0 2 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237778084 G A 0 0 4 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -5.07 +chr1 237780626 G A 0 0 1 RYR2 2.6 0 0 9.88 0 0 0 1.54 0 0 1.715 0 0 15.735 +chr1 237789101 T C 0 0 1 RYR2 2.6 0 0 19.76 0 0 0 1.54 0 0 1.715 0 0 25.615 +chr1 237801770 T C 37 0 74 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237802395 G C 0 0 1 RYR2 2.6 0 2.09 19.76 0 0 0 1.54 0 0 6.86 0 0 32.85 +chr1 237811766 C T 0 0 1 RYR2 2.6 0 -1.045 0 0 0 0 1.54 0 0 0 0 0 3.095 +chr1 237814783 C T 7 0 35 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237823256 A C 0 0 5 RYR2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 237829952 G A 0 0 1 RYR2 2.6 0 0 0 0 0 0 1.54 0 0 0 0 0 4.14 +chr1 237841390 A G 4 0 20 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 4.58 0 1.715 0 0 -0.490000000000001 +chr1 237850716 C T 0 0 1 RYR2 2.6 0 0 0 0 0 0 1.54 4.58 0 0 0 0 8.72 +chr1 237863718 T G 37 0 74 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237872887 T C 0 0 3 RYR2 2.6 2.09 0 -9.88 0 0 0 0 0 0 0 0 0 -5.19 +chr1 237875068 C T 0 0 1 RYR2 2.6 0 -1.045 0 0 0 0 1.54 0 0 0 0 0 3.095 +chr1 237881770 C T 36 0 73 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237890437 C T 36 0 73 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237893674 C T 37 0 74 RYR2 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 237905568 TCCTTTTTTTTTTTTTTTAAATATACA TCCCTTTTTTTTTTTTTTTAAATATACA,TCCCTTTTTTTTTTTTTTAAATATACA,TCCTTTTTTTTTTTTTTAAATATACA,TCCTTTTTTTTTTTTTTTTAAATATACA 0 2 74 RYR2 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 237905570 CTTTTTTTTTTTTTTTAAATATACA CTTTTTTTTTTTTTTTTAAATATACA,CTTTTTTTTTTTTTTAAATATACA 0 0 74 RYR2 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 237905571 T C 0 0 1 RYR2 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 237923053 C T 22 0 56 RYR2 2.6 0 0 -9.88 0 0 3.36 1.54 0 0 0 0 0 -2.38 +chr1 237923081 G A 0 0 1 RYR2 2.6 0 0 19.76 0 0 3.36 1.54 0 0 3.43 0 0 30.69 +chr1 237924352 G A 0 0 1 RYR2 2.6 0 0 19.76 0 0 3.36 1.54 0 0 0 0 0 27.26 +chr1 237941945 G A 0 0 3 RYR2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 237942082 AACTGCCTT ACCTT 0 0 3 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237946964 T C 3 0 19 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237947000 C T 0 0 3 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237948286 A G 0 0 2 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237951451 A G 7 0 31 RYR2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 237957146 G A 13 0 42 RYR2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 237957161 A G 14 0 43 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237957309 A C 13 0 41 RYR2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chr1 237965131 GCATTTTTTTTTTTTGTCATTG ACATTTTTTTTTTTTTGTCATTG,ACATTTTTTTTTTTTTTTGTCATTG,ACATTTTTTTTTTTTTTGTCATTG 3 1 41 RYR2 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 8.26 32.16 +chr1 237965133 ATTTTTTTTTTTTGTCATTG ATTTTTTTTTTTGTCATTG 0 0 1 RYR2 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chr1 237972189 A G 0 0 2 RYR2 2.6 0 -1.045 0 0 0 0 1.54 0 0 0 0 4.13 7.225 +chr1 237982383 C A 0 0 1 RYR2 2.6 0 -2.09 0 0 0 0 1.54 0 0 0 0 0 2.05 +chr1 237991767 T C 0 0 2 RYR2 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr1 237993877 G C 0 0 1 RYR2 2.6 0 2.09 19.76 0 0 0 1.54 0 0 0 0 0 25.99 +chr10 18430167 G C 1 0 2 CACNB2 0 0 0 -9.88 0 0 3.36 1.54 4.58 0 0 0 0 -0.400000000000001 +chr10 18439769 AATAATCTTATTTGTCTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG AATAATCTTATTTGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 0 2 CACNB2 0 0 0 19.76 0 0 0 1.54 0 0 0 0 4.13 25.43 +chr10 18439775 CTTATTTGTCTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG CTTATTTGTCTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG,TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG 3 0 2 CACNB2 0 0 0 19.76 0 0 0 0 0 0 0 0 4.13 23.89 +chr10 18439777 TATTTGTCTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG TATTTGTCTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG 1 0 2 CACNB2 0 0 0 0 0 0 0 0 0 0 0 0 4.13 4.13 +chr10 18439779 TTTGTCTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG 1 0 2 CACNB2 0 0 0 19.76 0 0 0 0 0 0 0 0 4.13 23.89 +chr10 18439784 CTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG TTTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG,CTTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG,CTTTTTTTTTTTTTTTTTTTTTTTAGTCATATGG 2 0 2 CACNB2 0 0 0 0 0 0 0 0 0 0 0 0 4.13 4.13 +chr10 18439810 AGTCATA TGTCATA,TTTTTTT 0 0 2 CACNB2 0 0 0 19.76 0 0 0 1.54 0 0 0 0 4.13 25.43 +chr10 18439926 T C 0 0 7 CACNB2 0 0 0 -9.88 0 0 0 0 0 0 0 0 0 -9.88 +chr10 18690063 TTATTTTGTCT TT 0 0 1 CACNB2 0 0 0 19.76 0 0 0 1.54 4.58 0 0 0 0 25.88 +chr10 18789724 T G 5 0 27 CACNB2 0 -2.09 0 -9.88 0 0 0 1.54 0 0 0 0 0 -10.43 +chr10 18803338 A G 0 0 2 CACNB2 0 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -8.34 +chr10 18816565 G A 0 0 2 CACNB2 0 2.09 2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -4.16 +chr10 18816633 C T 1 0 11 CACNB2 0 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -9.385 +chr10 18828371 C T 1 0 11 CACNB2 0 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -9.385 +chr10 18828635 T G 2 0 25 CACNB2 0 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -9.385 +chr10 18828661 CCG CCT 2 0 4 CACNB2 0 0 0 19.76 0 0 0 1.54 0 0 0 0 8.26 29.56 +chr10 18828662 CG CT 3 0 7 CACNB2 0 0 0 19.76 0 0 0 1.54 0 0 0 0 8.26 29.56 +chr10 18828663 G T 21 0 51 CACNB2 0 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 6.13 0 -4.3 +chr10 18828669 GTTTTTTTTTTTTTTTTTTTGAAGTC GTTTTTTTTTTTTTTTTTTGAAGTC,GTTTTTTTTTTTTTTTTTGAAGTC,GCTTTTTTTTTTTTTTTTTGAAGTC,GTTTTTTTTTTTTTTTTGAAGTC,GCTTTTTTTTTTTTTTTTTTGAAGTC,TTTTTTTTTTTTTTTTTTTTGAAGTC 5 7 51 CACNB2 0 0 0 19.76 0 0 0 1.54 0 0 0 0 8.26 29.56 +chr10 18828670 T C 0 0 12 CACNB2 0 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -9.385 +chr10 21074724 T C 0 0 8 NEBL 2.6 0 -2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr10 21076100 C A 0 0 1 NEBL 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr10 21097546 G A 0 0 1 NEBL 2.6 0 -1.045 0 0 0 0 1.54 0 0 3.43 0 0 6.525 +chr10 21106525 A G 0 0 1 NEBL 2.6 0 0 0 0 0 0 1.54 0 0 0 0 0 4.14 +chr10 21106567 G C 0 0 1 NEBL 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 0 23.9 +chr10 21108377 C T 2 0 16 NEBL 2.6 0 -2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr10 21108395 C T 0 0 1 NEBL 2.6 0 -1.045 19.76 0 0 0 1.54 0 0 0 0 0 22.855 +chr10 21112111 A T 3 0 18 NEBL 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr10 21112137 A T 0 0 1 NEBL 2.6 0 -2.09 -9.88 0 3.985 0 0 0 0 1.715 0 0 -3.67 +chr10 21115347 A G 0 0 2 NEBL 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr10 21120096 G A 0 0 1 NEBL 2.6 0 0 0 0 0 3.36 0 0 0 0 0 0 5.96 +chr10 21120116 A G 5 0 25 NEBL 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr10 21134282 C G 1 0 10 NEBL 2.6 0 -2.09 -9.88 0 0 0 3.08 0 0 3.43 0 0 -2.86 +chr10 21139389 T C 1 0 10 NEBL 2.6 0 -2.09 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr10 21141440 AGGGAGGGT AGGAGGGT 2 0 14 NEBL 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr10 21141469 T C 37 0 74 NEBL 2.6 0 -2.09 -9.88 0 0 0 0 0 0 0 0 0 -9.37 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AAAATATATATATATATATATATATATATATAG,AAAATATATATATATATATATATATATATAG,AAAATATATGTATATATAG,AAAATATATATATATATATATATATATATATATAG,AAAATATATATATATATATATATATATATATATATAG,AAAATAAATAAATATATATATATATATATATATATATAG 1 3 12 ANKRD1 2.6 0 0 -9.88 0 0 0 0 4.58 0 0 0 0 -2.7 +chr10 92678740 AATAAATAAATATATATATATATATATATATATAG AATATATGTATATATAG,AATATATATAG,AATATATATATATATAG,AATATATATATATATATATATATATATAG,AATATATATATATATATATATATATATATATAG,AATATATGTATATATAGCATGAGAGATATATATATAG,AATATATATATATATATATATATATATATATATAG,AATATATGTATATATAGCATGATATATATATATATAG 4 12 12 ANKRD1 2.6 0 0 19.76 0 0 0 0 4.58 0 0 0 8.26 35.2 +chr10 92678744 AATAA TATGT,TATAT 1 0 12 ANKRD1 2.6 0 0 19.76 0 0 0 0 4.58 0 0 0 8.26 35.2 +chr10 92678755 ATATATAT AGCATGAGAG 0 0 1 ANKRD1 2.6 0 0 19.76 0 0 0 0 4.58 0 0 0 0 26.94 +chr10 92678756 T G 0 0 1 ANKRD1 2.6 0 0 19.76 0 0 0 0 4.58 0 0 0 0 26.94 +chr10 92678765 A G 6 0 27 ANKRD1 2.6 0 0 -9.88 0 0 0 0 4.58 0 0 0 0 -2.7 +chr10 101473218 A G 32 0 68 COX15 0 0 0 -9.88 0 0 0 0 0 0 1.715 0 0 -8.165 +chr10 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179585393 A G 1 0 4 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 0 0 0 0 6.13 0 -3.24 +chr2 179587130 C G 1 0 4 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 4.58 0 0 6.13 0 2.88 +chr2 179589058 G A 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr2 179593270 A G 0 0 1 TTN 2.6 2.09 2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -1.56 +chr2 179593352 C T 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr2 179593503 G T 0 0 1 TTN 2.6 -1.045 0 0 0 0 0 1.54 0 0 3.43 0 0 6.525 +chr2 179595117 C G 1 0 4 TTN 2.6 0 0 -9.88 0 0 0 0 0 0 0 6.13 0 -1.15 +chr2 179595372 T C 0 0 1 TTN 2.6 2.09 2.09 -9.88 0 0 0 1.54 0 0 1.715 0 0 0.154999999999999 +chr2 179597007 T C 0 0 1 TTN 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 0 23.9 +chr2 179598139 C A 0 0 1 TTN 2.6 0 0 19.76 0 0 0 1.54 0 0 3.43 0 0 27.33 +chr2 179598228 A G 0 0 3 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179600563 G A 13 0 26 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179605180 C T 1 0 4 TTN 2.6 0 -2.09 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0 -9.88 0 0 0 1.54 0 0 1.715 0 0 -4.025 +chr2 179623758 C T 12 0 25 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr2 179629363 T C 13 0 26 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179629461 C T 12 0 25 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179631214 T C 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179632496 T C 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr2 179632710 T C 9 0 21 TTN 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr2 179633644 G C 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179634392 A T 1 0 4 TTN 2.6 2.09 2.09 0 0 0 0 0 0 0 0 0 8.26 15.04 +chr2 179634839 T C 0 0 1 TTN 2.6 -1.045 0 0 0 0 0 1.54 0 0 0 0 0 3.095 +chr2 179635919 C T 0 0 2 TTN 2.6 0 0 -9.88 0 0 0 0 0 0 0 0 0 -7.28 +chr2 179638238 G A 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179638314 CGGT CGC 0 0 1 TTN 2.6 0 0 19.76 7.59 0 0 1.54 0 0 0 0 0 31.49 +chr2 179638721 C T 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 3.43 0 0 -4.4 +chr2 179641009 C T 0 0 1 TTN 2.6 0 0 9.88 0 0 0 1.54 0 0 0 0 0 14.02 +chr2 179642425 G A 12 0 25 LOC101927055 0 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -10.43 +chr2 179644035 G A 12 0 25 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr2 179644855 T C 10 0 23 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 1.715 0 0 -6.115 +chr2 179650408 G A 0 0 7 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 3.43 0 0 -4.4 +chr2 179650443 C T 0 0 1 TTN 2.6 -1.045 0 19.76 0 0 0 1.54 0 0 0 0 0 22.855 +chr2 179650701 C T 3 0 12 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179659108 T C 0 0 1 TTN 2.6 0 0 0 0 0 0 0 0 0 0 0 0 2.6 +chr2 179659294 C T 0 0 1 TTN 2.6 0 0 0 0 0 0 1.54 0 0 0 0 0 4.14 +chr2 179659912 G A 0 0 1 TTN 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chr2 179669244 GAAAAAAAAACAAAAGTG GAAAAAAAAAACAAAAGTG 0 0 1 TTN 2.6 0 0 0 0 0 0 1.54 4.58 0 0 0 0 8.72 +chr2 220283259 A G 12 0 24 DES 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G A 0 0 4 MYLK2 0 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -8.34 +chr20 30414621 C T 0 0 3 MYLK2 0 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -10.43 +chr20 30419834 C T 0 0 1 MYLK2 0 0 0 19.76 0 0 0 1.54 0 0 0 0 0 21.3 +chr20 30419954 A G 0 0 10 MYLK2 0 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -9.385 +chr20 31996708 A G 0 0 1 SNTA1 0 0 0 9.88 0 0 0 1.54 0 0 0 0 0 11.42 +chr20 32031112 C A 0 0 1 SNTA1 0 0 0 19.76 0 7.97 3.36 1.54 4.58 0 0 0 0 37.21 +chr20 32031206 G A 0 0 1 SNTA1 0 0 2.09 0 0 0 3.36 1.54 4.58 0 0 0 0 11.57 +chr20 32031208 C A 1 0 2 SNTA1 0 0 0 19.76 0 0 3.36 1.54 4.58 0 0 0 4.13 33.37 +chr20 42743454 A G 1 0 18 JPH2 2.6 -2.09 -2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -9.92 +chr20 42744587 G C 0 0 11 JPH2 2.6 -2.09 -2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -9.92 +chr20 42744802 C T 0 0 2 JPH2 2.6 -2.09 -2.09 -9.88 0 0 0 1.54 0 0 1.715 0 0 -8.205 +chr20 42744945 G A 0 0 1 JPH2 2.6 0 0 19.76 0 0 0 1.54 0 0 1.715 0 0 25.615 +chr20 42745033 G A 0 0 1 JPH2 2.6 -2.09 -2.09 -9.88 0 0 0 1.54 0 0 0 0 0 -9.92 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0 0 5.41 +chr22 19867771 C T 2 0 12 TXNRD2 2.6 0 -2.09 -9.88 0 0 3.36 1.54 0 0 0 6.13 0 1.66 +chr22 19868218 A G 20 0 52 TXNRD2 2.6 0 -2.09 -9.88 0 0 3.36 1.54 4.58 0 0 0 0 0.109999999999999 +chr22 19868255 AGGGGGGCCA AGGGGGCCA 2 0 12 TXNRD2 2.6 0 0 -9.88 0 0 3.36 0 4.58 0 0 0 0 0.659999999999999 +chr22 19870831 C T 4 0 24 TXNRD2 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 6.13 0 2.21 +chr22 19870995 CAGAGAGG CAGAGG 0 0 1 TXNRD2 2.6 0 0 19.76 0 0 3.36 0 0 0 0 0 0 25.72 +chr22 19882976 G T 0 0 1 TXNRD2 2.6 0 -2.09 -9.88 0 0 3.36 0 0 0 0 0 0 -6.01 +chr22 19882984 T G 3 0 15 TXNRD2 2.6 0 -2.09 -9.88 0 0 3.36 0 0 0 1.715 12.26 0 7.965 +chr22 19885548 G T 3 0 15 TXNRD2 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 12.26 0 8.34 +chr22 19898886 C T 1 0 10 TXNRD2 2.6 0 0 -9.88 0 0 3.36 0 0 0 0 0 0 -3.92 +chr22 19902718 ATG AG 0 0 1 TXNRD2 2.6 0 0 0 0 0 3.36 0 0 0 0 0 0 5.96 +chr22 19903290 C G 0 0 1 TXNRD2 2.6 0 -2.09 -9.88 0 7.97 3.36 1.54 0 0 1.715 0 0 5.215 +chr22 19905801 CG CA 2 0 4 TXNRD2 2.6 0 0 19.76 0 0 3.36 0 0 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0 0 -4.4 +chr7 128477472 T C 1 0 2 FLNC 0 0 0 -9.88 0 0 3.36 1.54 0 0 0 0 0 -4.98 +chr7 150645534 T G 1 0 7 KCNH2 2.6 0 -1.045 -9.88 0 0 3.36 1.54 0 0 1.715 0 0 -1.71 +chr7 150648198 A G 7 0 18 KCNH2 2.6 0 -1.045 -9.88 0 0 3.36 1.54 0 0 0 0 0 -3.425 +chr7 150648789 T C 2 0 10 KCNH2 2.6 0 -1.045 -9.88 0 0 3.36 1.54 4.58 0 0 0 0 1.155 +chr7 150649531 G A 0 0 8 KCNH2 2.6 -1.045 -1.045 -9.88 0 0 3.36 1.54 0 0 0 0 0 -4.47 +chr7 150649603 G A 0 0 8 KCNH2 2.6 0 -1.045 -9.88 0 0 3.36 1.54 0 0 0 0 0 -3.425 +chr7 150655219 C T 1 0 2 KCNH2 2.6 0 0 19.76 0 0 3.36 1.54 0 0 6.86 0 4.13 38.25 +chr7 150655361 C A 1 0 2 KCNH2 2.6 0 0 19.76 0 0 3.36 1.54 0 0 0 0 4.13 31.39 +chr7 151262385 T C 0 0 5 PRKAG2 0 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -8.34 +chr7 151262528 A C 0 0 1 PRKAG2 0 0 0 0 0 0 0 1.54 0 0 0 0 0 1.54 +chr7 151267353 G A 0 0 3 PRKAG2 0 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -8.34 +chr7 151329255 A G 0 0 1 PRKAG2 0 0 0 19.76 0 0 3.36 1.54 4.58 0 0 0 0 29.24 +chr7 151573580 G A 0 0 2 PRKAG2 0 0 -1.045 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31224684 A G 31 0 64 DMD 2.6 -1.045 0 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chrX 31496350 C T 32 0 65 DMD 2.6 0 0 -9.88 0 0 0 1.54 0 0 1.715 0 0 -4.025 +chrX 31496426 T C 1 0 2 DMD 2.6 2.09 2.09 -9.88 0 0 0 1.54 0 0 1.715 0 0 0.154999999999999 +chrX 31496431 T A 1 0 2 DMD 2.6 2.09 2.09 -9.88 0 0 0 1.54 0 0 3.43 0 0 1.87 +chrX 31676096 G A 10 0 25 DMD 2.6 -1.045 0 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chrX 31697636 A G 3 0 9 DMD 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -7.83 +chrX 31893307 T G 7 0 19 DMD 2.6 0 0 -9.88 7.59 0 0 1.54 0 0 0 0 0 1.85 +chrX 31986499 G A 1 0 2 DMD 2.6 0 2.09 0 0 0 0 1.54 0 0 3.43 0 4.13 13.79 +chrX 32380996 C T 10 0 25 DMD 2.6 -1.045 -1.045 -9.88 0 0 0 1.54 0 0 3.43 0 0 -4.4 +chrX 32408311 T C 2 0 7 DMD 2.6 -1.045 0 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chrX 32456458 C T 1 0 2 DMD 2.6 0 0 19.76 0 0 0 1.54 0 0 3.43 0 4.13 31.46 +chrX 32459449 A G 1 0 2 DMD 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chrX 32472763 CTTTTTTTTTTTTTACCTTCA 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0 9 KCNE5 0 0 0 -9.88 0 0 0 1.54 4.58 0 1.715 0 0 -2.045 +chrX 119573169 G A 0 0 1 LAMP2 2.6 0 0 0 0 0 0 1.54 0 0 0 0 0 4.14 +chrX 119576454 C T 0 0 1 LAMP2 2.6 0 0 19.76 0 7.97 0 1.54 4.58 0 0 0 0 36.45 +chrX 119576455 G A 1 0 4 LAMP2 2.6 0 -1.045 -9.88 0 0 0 1.54 4.58 0 0 0 0 -2.205 +chrX 119590533 T A 12 0 30 LAMP2 2.6 0 -1.045 -9.88 0 0 0 1.54 0 0 0 0 0 -6.785 +chrX 135279350 C A 0 0 1 FHL1 2.6 0 0 19.76 0 0 0 1.54 4.58 0 0 0 0 28.48 +chrX 135292022 C T 10 0 27 FHL1 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chrX 153640406 C T 9 0 22 DNASE1L1 0 0 0 -9.88 0 0 3.36 0 9.16 0 0 12.26 0 14.9 +chrX 153641619 C T 0 0 3 TAZ 2.6 0 0 -9.88 0 0 0 1.54 0 0 0 0 0 -5.74 +chrX 153648032 C T 1 0 2 TAZ 2.6 0 0 19.76 0 0 3.36 1.54 0 0 0 0 4.13 31.39 +chrX 153648156 C T 1 0 2 TAZ 2.6 0 0 19.76 0 0 3.36 1.54 0 0 0 0 4.13 31.39 +chr3 12626632 T G 0 0 3 RAF1 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 4.13 28.03 +chr12 32974391 CA C 1 0 4 PKP2 2.6 0 0 19.76 7.59 0 0 1.54 0 0 0 0 8.26 39.75 +chr7 91726576 C T 0 0 3 AKAP9 2.6 0 0 19.76 7.59 0 0 1.54 0 0 0 0 4.13 35.62 +chr7 91737871 C G 1 0 2 AKAP9 2.6 0 0 19.76 7.59 0 0 1.54 0 0 0 0 4.13 35.62 +chr6 7569521 G GG 0 0 1 DSP 2.6 0 0 19.76 7.59 0 0 1.54 9.16 0 0 0 0 40.65 +chr1 156100468 TCTGCTGAAC TCTGCTGAACTCTGCTGAAC 0 0 7 LMNA 2.6 0 0 19.76 7.59 0 3.36 3.08 0 0 0 0 8.26 44.65 +chr11 47369407 C T 1 0 2 MYBPC3 2.6 0 4.18 19.76 7.59 7.97 0 1.54 0 0 0 0 4.13 47.77 +chr1 78401653 AAAT A 5 0 14 NEXN 2.6 0 0 19.76 0 0 0 1.54 0 0 0 0 8.26 32.16 +chr12 33030841 CCGCCTGGCCGA C 1 0 2 PKP2 2.6 0 0 19.76 7.59 0 0 1.54 4.58 0 0 0 4.13 40.2 +chr2 179434234 AC A 1 0 4 TTN 2.6 0 0 19.76 7.59 0 0 1.54 0 0 0 0 8.26 39.75
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_heat_score.R Thu Sep 17 09:40:37 2020 +0000 @@ -0,0 +1,12 @@ +#!/usr/bin/env Rscript +args <- commandArgs(trailingOnly = TRUE) +file1=args[1] +cutoff=as.numeric(args[2]) +ofile=args[3] +data=read.table(file1,header=T,sep="\t") +rownames(data)=paste(data[,1], data[,2], data[,3], data[,4] ,sep="_") +png(ofile,width=1600,height=1800) +heatmap(as.matrix(data[data$ScoreT>=cutoff,9:21]),scale="row",col=colorRampPalette(c("white","purple","magenta"))(100),mar=c(12,16),cexRow=1.2,cexCol=2.5) +dev.off() + +