|
0
|
1 <tool id="gfap_r1.0_cdsvar_functional_annotater" name="Map to dbNSFP features">
|
|
|
2 <description>Annotate ms-/ns-SNVs with dbNSFP scores</description>
|
|
|
3 <command interpreter="perl">gfap_r1.0_cdsvar_functional_annotater.pl -varfile=$varfile -buildver=$buildver -dbdir=db/dbnsfp -release=$release -outdir=$__new_file_path__/gfap -outfile=$outfile</command>
|
|
|
4 <inputs>
|
|
|
5 <param name="varfile" format="txt" type="data" label="Input CDS file" />
|
|
|
6 <param name="buildver" type="select" label="Human reference genome assembly">
|
|
|
7 <option value="hg19">GRCh37 ie. hg19</option>
|
|
|
8 </param>
|
|
|
9 <param name="release" type="select" label="dbNSFP data release">
|
|
|
10 <option value="light1.3">v1.3</option>
|
|
|
11 <option value="light1.2">v1.2</option>
|
|
|
12 <option value="light1.1">v1.1</option>
|
|
|
13 <option value="light">v1.0</option>
|
|
|
14 </param>
|
|
|
15 </inputs>
|
|
|
16 <outputs>
|
|
|
17 <data format="txt" name="outfile" label="${varfile.name}.dbnsfp" />
|
|
|
18 </outputs>
|
|
|
19 <help>
|
|
|
20 .. class:: infomark
|
|
|
21
|
|
|
22 **What it does**
|
|
|
23
|
|
|
24 Annotate **mis-/non-sense** SNVs with **functional impact scores** of the **dbNSFP** database.
|
|
|
25
|
|
|
26 Input CDS-file has to be generated by the **Map_to_genomic_features** gfap utility.
|
|
|
27
|
|
|
28 .. class:: infomark
|
|
|
29
|
|
|
30 **Third-party resources**
|
|
|
31
|
|
|
32 dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
|
|
|
33
|
|
|
34 ----
|
|
|
35
|
|
|
36 **Input .cds file**::
|
|
|
37
|
|
|
38 #chr start end ref alt NRF NRR NAF NAR DP AD AF QC P.str P.ref P.alt VCF.FILTER DPT.FILTER VAR.FILTER AF_ALL AF_AFR AF_AMR AF_ASN AF_EUR AF_COS cid rs dbsnp annot ogs cos mid pid c.x p.x
|
|
|
39 chr1 69270 69270 A G 0 0 31 0 31 31 1.0000 179 3.10e-10 3.33e-01 3.10e-10 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss OR4F5 TRUE NM_001005484 NP_001005484 c.A180G p.S60S
|
|
|
40 chr1 69511 69511 A G 0 0 13 12 25 25 1.0000 222 3.33e-01 3.33e-01 3.33e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns OR4F5 TRUE NM_001005484 NP_001005484 c.A421G p.T141A
|
|
|
41 chr1 69897 69897 T C 1 0 0 3 4 3 0.7500 14 2.08e-01 3.33e-01 8.33e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss OR4F5 TRUE NM_001005484 NP_001005484 c.T807C p.S269S
|
|
|
42 chr1 881627 881627 G A 0 0 3 8 11 11 1.0000 88 7.55e-02 3.33e-01 7.55e-02 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss NOC2L TRUE NM_015658 NP_056473 c.C1843T p.L615L
|
|
|
43 chr1 887801 887801 A G 0 0 6 0 6 6 1.0000 56 1.04e-02 3.33e-01 1.04e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss NOC2L TRUE NM_015658 NP_056473 c.T1182C p.T394T
|
|
|
44 chr1 888639 888639 T C 0 0 4 9 13 13 1.0000 142 8.89e-02 3.33e-01 8.89e-02 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss NOC2L TRUE NM_015658 NP_056473 c.A918G p.E306E
|
|
|
45 chr1 888659 888659 T C 0 0 3 9 12 12 1.0000 146 4.87e-02 3.33e-01 4.87e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns NOC2L TRUE NM_015658 NP_056473 c.A898G p.I300V
|
|
|
46 chr1 897325 897325 G C 0 0 9 11 20 20 1.0000 188 2.75e-01 3.33e-01 2.75e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss KLHL17 TRUE NM_198317 NP_938073 c.G609C p.A203A
|
|
|
47 chr1 909238 909238 G C 0 0 3 5 8 8 1.0000 130 2.42e-01 3.33e-01 2.42e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns PLEKHN1 FALSE NM_032129|NM_001160184 NP_115505|NP_001153656 c.G1460C|c.G1355C p.R487P|p.R452P
|
|
|
48 chr1 909242 909242 A G 2 4 1 2 9 3 0.3330 15 1.69e-01 2.29e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss PLEKHN1 FALSE NM_032129|NM_001160184 NP_115505|NP_001153656 c.A1464G|c.A1359G p.G488G|p.G453G
|
|
|
49 chr1 935222 935222 C A 0 0 0 2 2 2 1.0000 10 1.67e-01 3.33e-01 1.67e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns HES4 FALSE NM_001142467 NP_001135939 c.G132T p.R44S
|
|
|
50 chr1 949654 949654 A G 0 0 11 9 20 20 1.0000 222 2.75e-01 3.33e-01 2.75e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss ISG15 TRUE NM_005101 NP_005092 c.A294G p.V98V
|
|
|
51 chr1 981931 981931 A G 0 0 1 1 2 2 1.0000 36 3.33e-01 3.33e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss AGRN TRUE NM_198576 NP_940978 c.A3066G p.S1022S
|
|
|
52 chr1 982994 982994 T C 0 0 13 16 29 29 1.0000 146 2.37e-01 3.33e-01 2.37e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss AGRN TRUE NM_198576 NP_940978 c.T3558C p.F1186F
|
|
|
53 chr1 1021346 1021346 A G 0 2 2 3 7 5 0.7140 66 1.51e-01 1.67e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ss C1orf159 FALSE NM_017891 NP_060361 c.T357C p.I119I
|
|
|
54
|
|
|
55 ----
|
|
|
56
|
|
|
57 **Output .dbnsfp file**::
|
|
|
58
|
|
|
59 #From [chr] to [p.x] = CDS file header
|
|
|
60 #AAS = Amino Acid Substitution(s)
|
|
|
61 #FIS = Functional Impact Score(s) from dbnsfp light1.3 release
|
|
|
62 #OCC = number of tools from which FIS was/were calculated
|
|
|
63 #FIS.max = highest score among FIS
|
|
|
64 #OCC.max = number of tools from which FIS.max was calculated
|
|
|
65 #PRED = qualitative ternary classifier ie. [L]ow; [M]edium; [H]igh
|
|
|
66 #chr start end ref alt NRF NRR NAF NAR DP AD AF QC P.str P.ref P.alt VCF.FILTER DPT.FILTER VAR.FILTER AF_ALL AF_AFR AF_AMR AF_ASN AF_EUR AF_COS cid rs dbsnp annot ogs cos mid pid c.x p.x AAS FIS OCC FIS.max OCC.max PRED
|
|
|
67 chr1 69511 69511 A G 0 0 13 12 25 25 1.0000 222 3.33e-01 3.33e-01 3.33e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns OR4F5 TRUE NM_001005484 NP_001005484 c.A421G p.T141A TA 0.38 5 0.38 5 M
|
|
|
68 chr1 888659 888659 T C 0 0 3 9 12 12 1.0000 146 4.87e-02 3.33e-01 4.87e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns NOC2L TRUE NM_015658 NP_056473 c.A898G p.I300V IV 0.46 4 0.46 4 M
|
|
|
69 chr1 909238 909238 G C 0 0 3 5 8 8 1.0000 130 2.42e-01 3.33e-01 2.42e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns PLEKHN1 FALSE NM_032129|NM_001160184 NP_115505|NP_001153656 c.G1460C|c.G1355C p.R487P|p.R452P RP 0.48 5 0.48 5 M
|
|
|
70 chr1 935222 935222 C A 0 0 0 2 2 2 1.0000 10 1.67e-01 3.33e-01 1.67e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns HES4 FALSE NM_001142467 NP_001135939 c.G132T p.R44S RS na na na na na
|
|
|
71 chr1 1269554 1269554 T C 0 0 5 1 6 6 1.0000 81 7.29e-02 3.33e-01 7.29e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns TAS1R3 TRUE NM_152228 NP_689414 c.T2269C p.C757R CR 0.35 5 0.35 5 M
|
|
|
72 chr1 1551927 1551927 T C 0 0 1 2 3 3 1.0000 40 3.33e-01 3.33e-01 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns MIB2 TRUE NM_080875:NM_001170688:NM_001170686:NM_001170687 NP_543151:NP_001164159:NP_001164157:NP_001164158 c.T214C p.F72L FL 0.06 4 0.06 4 L
|
|
|
73 chr1 1599812 1599812 C T 5 0 13 13 31 26 0.8390 225 1.58e-01 2.08e-02 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns SLC35E2B FALSE NM_001110781 NP_001104251 c.G934A p.V312I VI 0.63 5 0.63 5 M
|
|
|
74 chr1 1650787 1650787 T C 104 22 69 10 205 79 0.3850 225 4.44e-25 2.02e-14 1.85e-12 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns CDK11A;CDK11B TRUE NM_024011;NM_033486|NM_033489 NP_076916;NP_277021|NP_277024 c.A335G;c.A335G|c.A233G p.H112R;p.H112R|p.H78R HR 0.32 3 0.32 3 M
|
|
|
75 chr1 1650797 1650797 A G 110 28 76 9 223 85 0.3810 157 1.46e-25 3.64e-13 8.02e-15 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns CDK11A;CDK11B TRUE NM_024011:NM_033529;NM_033489|NM_033486 NP_076916:NP_277071;NP_277024|NP_277021 c.T325C;c.T223C|c.T325C p.C109R;p.C75R|p.C109R CR 0.33 3 0.33 3 M
|
|
|
76 chr1 1650832 1650832 A G 114 34 88 14 250 102 0.4080 138 3.92e-24 8.97e-12 9.25e-15 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns CDK11A;CDK11B TRUE NM_024011:NM_033529;NM_033489:NM_033488|NM_033486:NM_033492:NM_033493 NP_076916:NP_277071;NP_277024:NP_277023|NP_277021:NP_277027:NP_277028 c.T290C;c.T188C|c.T290C p.V97A;p.V63A|p.V97A VA 0.49 4 0.49 4 M
|
|
|
77 chr1 1650845 1650845 G A 93 25 100 36 254 136 0.5350 178 1.26e-17 7.09e-11 1.24e-08 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns CDK11A;CDK11B TRUE NM_024011:NM_033529;NM_033486:NM_033492:NM_033493|NM_033489:NM_033488 NP_076916:NP_277071;NP_277021:NP_277027:NP_277028|NP_277024:NP_277023 c.C277T;c.C277T|c.C175T p.R93W;p.R93W|p.R59W RW 0.97 4 0.97 4 H
|
|
|
78 chr1 1666251 1666251 G A 0 10 8 3 21 11 0.5240 136 1.28e-01 6.51e-04 7.55e-02 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns SLC35E2 TRUE NM_001199787:NM_182838 NP_001186716:NP_878258 c.C610T p.R204W RW 0.49 4 0.49 4 M
|
|
|
79 chr1 1686040 1686040 G T 10 2 17 3 32 20 0.6250 105 3.77e-05 1.29e-02 8.59e-04 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns NADK TRUE NM_023018:NM_001198993|NM_001198994|NM_001198995 NP_075394:NP_001185922|NP_001185923|NP_001185924 c.C786A|c.C1221A|c.C690A p.N262K|p.N407K|p.N230K NK 0.58 5 0.58 5 M
|
|
|
80 chr1 1849529 1849529 A G 3 9 6 6 24 12 0.5000 206 1.02e-01 4.87e-02 3.33e-01 NONE PASS SKIP 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na ns TMEM52 FALSE NM_178545 NP_848640 c.T422C p.M141T MT 0.50 5 0.50 5 M
|
|
|
81 chr1 1887019 1887019 A G 28 25 26 20 99 46 0.4650 150 1.41e-01 2.61e-01 1.54e-01 NONE PASS PASS 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 na na na sl KIAA1751 TRUE NM_001080484 NP_001073953 c.T2287C p.X763Q XQ na na na na na
|
|
|
82
|
|
|
83 ----
|
|
|
84
|
|
|
85 .. class:: infomark
|
|
|
86
|
|
|
87 **Feedback**: romain.daveau@curie.fr
|
|
|
88 </help>
|
|
|
89 </tool> |
