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Atarva regions (#185)
## Description Adding atarva region files to allow STRchive loci to be genotyped with atarva Still to do: - [x] Test region files - [x] Get feedback from atarva team (in progress at SowpatiLab/ATaRVa#3) - [ ] Add links on the STRchive website - [x] Consider adjusting directory structure as data dir is getting quite full? ## Major Changes - Generate atarva regions files ## Minor Changes - lock snakemake=7.25.0 to avoid this bug snakemake/snakemake#3289 ## Checklist - [x] All changes are well summarized - [x] Check all tests pass - [ ] Check that the website preview looks good - [ ] Update the STRchive version in `CITATION.cff`, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X. - [x] Ask someone to review this PR
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‎data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed‎

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#chrom start stop motif motif_len id
2+
chr1 870158 870178 GGCGCGGAGC 10 HMNR7_VWA1
3+
chr1 57245935 57245973 GAAAT 5 SCA37_DAB1
4+
chr1 94266544 94266567 GCC 3 OPDM_ABCD3
5+
chr1 148519695 148519738 GGC 3 NIID_NOTCH2NLC
6+
chr1 154328121 154330802 GGCTNNGGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG 61 ADTKD_MUC1
7+
chr1 155728131 155728159 GGGCC 5 NME_NAXE
8+
chr2 96703674 96703732 AAATG 5 FAME2_STARD7
9+
chr2 100563685 100563738 GCC 3 FRA2A_AFF3
10+
chr2 176581179 176581224 GCN 3 SD5_HOXD13
11+
chr2 191369982 191370024 GCA 3 GDPAG_GLS
12+
chr3 63956302 63956333 CAG 3 SCA7_ATXN7
13+
chr3 63956333 63956345 CCG 3 SCA7_ATXN7_flank
14+
chr3 131917482 131917557 CAGG 4 DM2_CNBP
15+
chr3 131917557 131917597 CAGA 4 DM2_CNBP_flank
16+
chr3 131917597 131917635 CA 2 DM2_CNBP_flank
17+
chr3 141687011 141687054 NGC 3 BPES_FOXL2
18+
chr3 186521667 186521706 TTTCA 5 FAME4_YEATS2
19+
chr4 3073603 3073687 CAG 3 HD_HTT
20+
chr4 3073687 3073693 CAACAG 6 HD_HTT_flank
21+
chr4 3073693 3073729 CCG 3 HD_HTT_flank
22+
chr4 39318077 39318136 AAGGG 5 CANVAS_RFC1
23+
chr4 41719745 41719805 GCN 3 CCHS_PHOX2B
24+
chr4 162693303 162693405 TTTCA 5 FAME7_RAPGEF2
25+
chr5 10295525 10295593 TTTCA 5 FAME3_MARCHF6
26+
chr5 147414733 147414780 GCT 3 SCA12_PPP2R2B
27+
chr6 16200188 16200282 CTG 3 SCA1_ATXN1
28+
chr6 45257567 45257618 GCN 3 CCD_RUNX2
29+
chr6 171935458 171935569 GCA 3 SCA17_TBP
30+
chr7 27335684 27335720 NGC 3 HFG_HOXA13-III
31+
chr7 27335813 27335849 NGC 3 HFG_HOXA13-II
32+
chr7 27335912 27335954 NGC 3 HFG_HOXA13-I
33+
chr7 56047900 56047939 GCG 3 FRA7A_ZNF713
34+
chr8 105716409 105716441 CGC 3 OPDM1_LRP12
35+
chr8 119495247 119495353 TGAAA 5 FAME1_SAMD12
36+
chr9 27584063 27584155 GGCCCC 6 FTDALS1_C9orf72
37+
chr9 81210834 81210861 GAA 3 FRDA_FXN
38+
chr9 81210861 81210877 A 1 FRDA_FXN_flank
39+
chr9 142886568 142886595 GCC 3 HSAN-VIII_PRDM12
40+
chr10 80695718 80695748 GGC 3 OPML1_NUTM2B-AS1
41+
chr11 119226662 119226696 CGG 3 JBS_CBL
42+
chr12 6947903 6947941 CAG 3 DRPLA_ATN1
43+
chr12 50468095 50468118 GGC 3 FRA12A_DIP2B
44+
chr12 111575873 111575940 CTG 3 SCA2_ATXN2
45+
chr12 123532573 123532603 GGC 3 OPDM4_RILPL1
46+
chr13 69361243 69361270 CTG 3 SCA8_ATXN8OS
47+
chr13 69361270 69361300 CTA 3 SCA8_ATXN8OS_flank
48+
chr13 99196358 99196404 GCN 3 HPE5_ZIC2
49+
chr13 101377549 101377792 GAA 3 SCA27B_FGF14
50+
chr14 17522488 17522519 GCN 3 OPMD_PABPN1
51+
chr14 86300519 86300603 CTG 3 SCA3_ATXN3
52+
chr15 20458510 20458536 GCG 3 ALS1_NIPA1
53+
chr15 86324038 86324057 TTTG 4 pre-MIR7-2_CHNG3
54+
chr15 87088411 87088452 GCT 3 CPEO_POLG
55+
chr16 17477909 17478002 GCC 3 DBQD2_XYLT1
56+
chr16 24890366 24890430 TTTCA 5 FAME6_TNRC6A
57+
chr16 72284666 72284761 TGGAA 5 SCA31_BEAN1
58+
chr16 73638636 73638724 CAG 3 SCA_THAP11
59+
chr16 78605502 78605569 GCC 3 SCA4_ZFHX3
60+
chr16 93675723 93675776 CTG 3 HDL2_JPH3
61+
chr17 17754961 17755053 TTTCA 5 FAME8_RAI1
62+
chr17 81047404 81047534 CCTCGCTGTGCCGCTGCCGA 20 RCPS_EIF4A3
63+
chr18 55789233 55789288 CAG 3 FECD3_TCF4
64+
chr19 13333136 13333176 CTG 3 SCA6_CACNA1A
65+
chr19 14622655 14622692 CCG 3 OPDM2_GIPC1
66+
chr19 18921630 18921645 GTC 3 EDM1-PSACH_COMP
67+
chr19 48597739 48597756 CAG 3 DM1_DMPK
68+
chr20 2683189 2683230 GGCCTG 6 SCA36_NOP56
69+
chr20 2683230 2683248 CGCCTG 6 SCA36_NOP56_flank
70+
chr20 4738633 4738705 CCTCATGGTGGTGGCTGGGGGCAG 24 CJD_PRNP
71+
chr20 4738705 4738732 CCTCAGGGCGGTGGTGGCTGGGGGCAG 27 CJD_PRNP_flank
72+
chr21 42132054 42132091 CGCGGGGCGGGG 12 EPM1_CSTB
73+
chr22 20143615 20143660 GCN 3 TOF_TBX1
74+
chr22 46280059 46280134 ATTCT 5 SCA10_ATXN10
75+
chrX 24597766 24597802 NGC 3 PRTS_ARX
76+
chrX 24597886 24597934 NGC 3 EIEE1_ARX
77+
chrX 30882677 30882743 TTC 3 DMD_DMD
78+
chrX 30882743 30882751 T 1 DMD_DMD_flank
79+
chrX 65975147 65975250 GCA 3 SBMA_AR
80+
chrX 69887153 69887230 AGAGGG 6 XDP_TAF1
81+
chrX 135876774 135876804 GCN 3 VACTERLX_ZIC3
82+
chrX 138816203 138816248 NGC 3 XLMR_SOX3
83+
chrX 146176677 146176769 CGG 3 FXS_FMR1
84+
chrX 146765190 146765342 GCC 3 FRAXE_AFF2

‎data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz‎

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‎data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz.tbi‎

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‎data/catalogs/STRchive-disease-loci.hg19.atarva.bed‎

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#chrom start stop motif motif_len id
2+
chr1 1371178 1371198 GGCGCGGAGC 10 HMNR7_VWA1
3+
chr1 57832715 57832793 GAAAT 5 SCA37_DAB1
4+
chr1 94883977 94884000 GCC 3 OPDM_ABCD3
5+
chr1 145209323 145209354 GGC 3 NIID_NOTCH2NLC
6+
chr1 155160981 155162030 GGCTNNGGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG 61 ADTKD_MUC1
7+
chr1 156561557 156561575 GGGCC 5 NME_NAXE
8+
chr2 96862804 96862862 AAATG 5 FAME2_STARD7
9+
chr2 100721260 100721286 GCC 3 FRA2A_AFF3
10+
chr2 176957786 176957831 GCN 3 SD5_HOXD13
11+
chr2 191745598 191745646 GCA 3 GDPAG_GLS
12+
chr3 63898360 63898391 CAG 3 SCA7_ATXN7
13+
chr3 63898391 63898403 CCG 3 SCA7_ATXN7_flank
14+
chr3 128891419 128891499 CAGG 4 DM2_CNBP
15+
chr3 128891499 128891539 CAGA 4 DM2_CNBP_flank
16+
chr3 128891539 128891577 CA 2 DM2_CNBP_flank
17+
chr3 138664861 138664904 NGC 3 BPES_FOXL2
18+
chr3 183429975 183430014 TTTCA 5 FAME4_YEATS2
19+
chr4 3076603 3076660 CAG 3 HD_HTT
20+
chr4 3076660 3076666 CAACAG 6 HD_HTT_flank
21+
chr4 3076666 3076702 CCG 3 HD_HTT_flank
22+
chr4 39350044 39350103 AAGGG 5 CANVAS_RFC1
23+
chr4 41747989 41748049 GCN 3 CCHS_PHOX2B
24+
chr4 160263678 160263770 TTTCA 5 FAME7_RAPGEF2
25+
chr5 10356455 10356523 TTTCA 5 FAME3_MARCHF6
26+
chr5 146258290 146258322 GCT 3 SCA12_PPP2R2B
27+
chr6 16327864 16327955 CTG 3 SCA1_ATXN1
28+
chr6 45390487 45390538 GCN 3 CCD_RUNX2
29+
chr6 170870994 170871105 GCA 3 SCA17_TBP
30+
chr7 27239297 27239351 NGC 3 HFG_HOXA13-III
31+
chr7 27239444 27239480 NGC 3 HFG_HOXA13-II
32+
chr7 27239543 27239585 NGC 3 HFG_HOXA13-I
33+
chr7 55955293 55955332 GCG 3 FRA7A_ZNF713
34+
chr8 105601198 105601227 CGC 3 OPDM1_LRP12
35+
chr8 119379051 119379157 TGAAA 5 FAME1_SAMD12
36+
chr9 27573482 27573544 GGCCCC 6 FTDALS1_C9orf72
37+
chr9 71652202 71652220 GAA 3 FRDA_FXN
38+
chr9 71652220 71652236 A 1 FRDA_FXN_flank
39+
chr9 133556992 133557028 GCC 3 HSAN-VIII_PRDM12
40+
chr10 81586139 81586160 GGC 3 OPML1_NUTM2B-AS1
41+
chr11 119076999 119077033 CGG 3 JBS_CBL
42+
chr12 7045879 7045938 CAG 3 DRPLA_ATN1
43+
chr12 50898784 50898807 GGC 3 FRA12A_DIP2B
44+
chr12 112036753 112036823 CTG 3 SCA2_ATXN2
45+
chr12 124018267 124018297 GGC 3 OPDM4_RILPL1
46+
chr13 70713515 70713561 CTG 3 SCA8_ATXN8OS
47+
chr13 70713561 70713591 CTA 3 SCA8_ATXN8OS_flank
48+
chr13 100637702 100637748 GCN 3 HPE5_ZIC2
49+
chr13 102813924 102814076 GAA 3 SCA27B_FGF14
50+
chr14 23790681 23790712 GCN 3 OPMD_PABPN1
51+
chr14 92537354 92537396 CTG 3 SCA3_ATXN3
52+
chr15 23086363 23086389 GCG 3 ALS1_NIPA1
53+
chr15 89112664 89112683 TTTG 4 pre-MIR7-2_CHNG3
54+
chr15 89876819 89876860 GCT 3 CPEO_POLG
55+
chr16 17564764 17564779 GCC 3 DBQD2_XYLT1
56+
chr16 24624759 24624853 TTTCA 5 FAME6_TNRC6A
57+
chr16 66524299 66524369 TGGAA 5 SCA31_BEAN1
58+
chr16 67876765 67876853 CAG 3 SCA_THAP11
59+
chr16 72821593 72821657 GCC 3 SCA4_ZFHX3
60+
chr16 87637888 87637935 CTG 3 HDL2_JPH3
61+
chr17 17711672 17711774 TTTCA 5 FAME8_RAI1
62+
chr17 78120808 78120938 CCTCGCTGTGCCGCTGCCGA 20 RCPS_EIF4A3
63+
chr18 53253384 53253460 CAG 3 FECD3_TCF4
64+
chr19 13318672 13318712 CTG 3 SCA6_CACNA1A
65+
chr19 14606853 14606887 CCG 3 OPDM2_GIPC1
66+
chr19 18896844 18896860 GTC 3 EDM1-PSACH_COMP
67+
chr19 46273462 46273524 CAG 3 DM1_DMPK
68+
chr20 2633378 2633403 GGCCTG 6 SCA36_NOP56
69+
chr20 2633403 2633421 CGCCTG 6 SCA36_NOP56_flank
70+
chr20 4680043 4680139 CCTCATGGTGGTGGCTGGGGGCAG 24 CJD_PRNP
71+
chr20 4680139 4680166 CCTCAGGGCGGTGGTGGCTGGGGGCAG 27 CJD_PRNP_flank
72+
chr21 45196323 45196360 CGCGGGGCGGGG 12 EPM1_CSTB
73+
chr22 19754285 19754330 GCN 3 TOF_TBX1
74+
chr22 46191234 46191304 ATTCT 5 SCA10_ATXN10
75+
chrX 25031646 25031682 NGC 3 PRTS_ARX
76+
chrX 25031766 25031814 NGC 3 EIEE1_ARX
77+
chrX 31302674 31302722 TTC 3 DMD_DMD
78+
chrX 31302722 31302730 T 1 DMD_DMD_flank
79+
chrX 66765158 66765261 GCA 3 SBMA_AR
80+
chrX 70672904 70672981 AGAGGG 6 XDP_TAF1
81+
chrX 136648985 136649015 GCN 3 VACTERLX_ZIC3
82+
chrX 139586481 139586526 NGC 3 XLMR_SOX3
83+
chrX 146993567 146993629 CGG 3 FXS_FMR1
84+
chrX 147582124 147582273 GCC 3 FRAXE_AFF2

‎data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz‎

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‎data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz.tbi‎

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‎data/catalogs/STRchive-disease-loci.hg38.atarva.bed‎

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#chrom start stop motif motif_len id
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chr1 1435798 1435818 GGCGCGGAGC 10 HMNR7_VWA1
3+
chr1 57367043 57367121 GAAAT 5 SCA37_DAB1
4+
chr1 94418421 94418444 GCC 3 OPDM_ABCD3
5+
chr1 149390802 149390842 GGC 3 NIID_NOTCH2NLC
6+
chr1 155188505 155192239 GGCTNNGGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG 61 ADTKD_MUC1
7+
chr1 156591765 156591783 GGGCC 5 NME_NAXE
8+
chr2 96197066 96197124 AAATG 5 FAME2_STARD7
9+
chr2 100104798 100104824 GCC 3 FRA2A_AFF3
10+
chr2 176093058 176093103 GCN 3 SD5_HOXD13
11+
chr2 190880872 190880920 GCA 3 GDPAG_GLS
12+
chr3 63912684 63912715 CAG 3 SCA7_ATXN7
13+
chr3 63912715 63912727 CCG 3 SCA7_ATXN7_flank
14+
chr3 129172576 129172656 CAGG 4 DM2_CNBP
15+
chr3 129172656 129172696 CAGA 4 DM2_CNBP_flank
16+
chr3 129172696 129172734 CA 2 DM2_CNBP_flank
17+
chr3 138946019 138946062 NGC 3 BPES_FOXL2
18+
chr3 183712187 183712226 TTTCA 5 FAME4_YEATS2
19+
chr4 3074876 3074933 CAG 3 HD_HTT
20+
chr4 3074933 3074939 CAACAG 6 HD_HTT_flank
21+
chr4 3074939 3074975 CCG 3 HD_HTT_flank
22+
chr4 39348424 39348483 AAGGG 5 CANVAS_RFC1
23+
chr4 41745972 41746032 GCN 3 CCHS_PHOX2B
24+
chr4 159342526 159342618 TTTCA 5 FAME7_RAPGEF2
25+
chr5 10356343 10356411 TTTCA 5 FAME3_MARCHF6
26+
chr5 146878727 146878759 GCT 3 SCA12_PPP2R2B
27+
chr6 16327633 16327724 CTG 3 SCA1_ATXN1
28+
chr6 45422750 45422801 GCN 3 CCD_RUNX2
29+
chr6 170561906 170562017 GCA 3 SCA17_TBP
30+
chr7 27199678 27199732 NGC 3 HFG_HOXA13-III
31+
chr7 27199825 27199861 NGC 3 HFG_HOXA13-II
32+
chr7 27199924 27199966 NGC 3 HFG_HOXA13-I
33+
chr7 55887600 55887639 GCG 3 FRA7A_ZNF713
34+
chr8 104588970 104588999 CGC 3 OPDM1_LRP12
35+
chr8 118366812 118366918 TGAAA 5 FAME1_SAMD12
36+
chr9 27573484 27573546 GGCCCC 6 FTDALS1_C9orf72
37+
chr9 69037286 69037304 GAA 3 FRDA_FXN
38+
chr9 69037304 69037320 A 1 FRDA_FXN_flank
39+
chr9 130681605 130681641 GCC 3 HSAN-VIII_PRDM12
40+
chr10 79826383 79826404 GGC 3 OPML1_NUTM2B-AS1
41+
chr11 119206289 119206323 CGG 3 JBS_CBL
42+
chr12 6936716 6936775 CAG 3 DRPLA_ATN1
43+
chr12 50505001 50505024 GGC 3 FRA12A_DIP2B
44+
chr12 111598949 111599019 CTG 3 SCA2_ATXN2
45+
chr12 123533720 123533750 GGC 3 OPDM4_RILPL1
46+
chr13 70139383 70139429 CTG 3 SCA8_ATXN8OS
47+
chr13 70139429 70139459 CTA 3 SCA8_ATXN8OS_flank
48+
chr13 99985448 99985494 GCN 3 HPE5_ZIC2
49+
chr13 102161574 102161726 GAA 3 SCA27B_FGF14
50+
chr14 23321472 23321503 GCN 3 OPMD_PABPN1
51+
chr14 92071010 92071052 CTG 3 SCA3_ATXN3
52+
chr15 22786677 22786703 GCG 3 ALS1_NIPA1
53+
chr15 88569433 88569452 TTTG 4 pre-MIR7-2_CHNG3
54+
chr15 89333588 89333629 GCT 3 CPEO_POLG
55+
chr16 17470907 17470922 GCC 3 DBQD2_XYLT1
56+
chr16 24613438 24613532 TTTCA 5 FAME6_TNRC6A
57+
chr16 66490396 66490466 TGGAA 5 SCA31_BEAN1
58+
chr16 67842862 67842950 CAG 3 SCA_THAP11
59+
chr16 72787694 72787758 GCC 3 SCA4_ZFHX3
60+
chr16 87604282 87604329 CTG 3 HDL2_JPH3
61+
chr17 17808358 17808460 TTTCA 5 FAME8_RAI1
62+
chr17 80147009 80147139 CCTCGCTGTGCCGCTGCCGA 20 RCPS_EIF4A3
63+
chr18 55586153 55586229 CAG 3 FECD3_TCF4
64+
chr19 13207858 13207898 CTG 3 SCA6_CACNA1A
65+
chr19 14496041 14496075 CCG 3 OPDM2_GIPC1
66+
chr19 18786034 18786050 GTC 3 EDM1-PSACH_COMP
67+
chr19 45770204 45770266 CAG 3 DM1_DMPK
68+
chr20 2652732 2652757 GGCCTG 6 SCA36_NOP56
69+
chr20 2652757 2652775 CGCCTG 6 SCA36_NOP56_flank
70+
chr20 4699397 4699493 CCTCATGGTGGTGGCTGGGGGCAG 24 CJD_PRNP
71+
chr20 4699493 4699520 CCTCAGGGCGGTGGTGGCTGGGGGCAG 27 CJD_PRNP_flank
72+
chr21 43776442 43776479 CGCGGGGCGGGG 12 EPM1_CSTB
73+
chr22 19766762 19766807 GCN 3 TOF_TBX1
74+
chr22 45795354 45795424 ATTCT 5 SCA10_ATXN10
75+
chrX 25013529 25013565 NGC 3 PRTS_ARX
76+
chrX 25013649 25013697 NGC 3 EIEE1_ARX
77+
chrX 31284557 31284605 TTC 3 DMD_DMD
78+
chrX 31284605 31284613 T 1 DMD_DMD_flank
79+
chrX 67545316 67545419 GCA 3 SBMA_AR
80+
chrX 71453054 71453131 AGAGGG 6 XDP_TAF1
81+
chrX 137566826 137566856 GCN 3 VACTERLX_ZIC3
82+
chrX 140504316 140504361 NGC 3 XLMR_SOX3
83+
chrX 147912049 147912111 CGG 3 FXS_FMR1
84+
chrX 148500604 148500753 GCC 3 FRAXE_AFF2

‎data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz‎

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‎data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz.tbi‎

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‎scripts/environment.yml‎

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- r-purrr
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- gfortran
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- pysam
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- htslib
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- bedtools
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- nodejs # build website locally
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- pyliftover
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- pip

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