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Merge pull request #78 from nf-core/77-add-liftover-option-for-truths
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77 add liftover option for truths
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kubranarci authored Aug 7, 2024
2 parents 6ebdb63 + 97ff2ba commit 97424ab
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Showing 43 changed files with 2,087 additions and 72 deletions.
25 changes: 25 additions & 0 deletions assets/rename_contigs/grch37_grch38.txt
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1 chr1
2 chr2
3 chr3
4 chr4
5 chr5
6 chr6
7 chr7
8 chr8
9 chr9
10 chr10
11 chr11
12 chr12
13 chr13
14 chr14
15 chr15
16 chr16
17 chr17
18 chr18
19 chr19
20 chr20
21 chr21
22 chr22
X chrX
Y chrY
M chrMT
194 changes: 194 additions & 0 deletions assets/rename_contigs/grch38_grch37.txt
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chr1 1
chr10 10
chr11 11
chr11_KI270721v1_random KI270721.1
chr12 12
chr13 13
chr14 14
chr14_GL000009v2_random GL000009.2
chr14_GL000194v1_random GL000194.1
chr14_GL000225v1_random GL000225.1
chr14_KI270722v1_random KI270722.1
chr14_KI270723v1_random KI270723.1
chr14_KI270724v1_random KI270724.1
chr14_KI270725v1_random KI270725.1
chr14_KI270726v1_random KI270726.1
chr15 15
chr15_KI270727v1_random KI270727.1
chr16 16
chr16_KI270728v1_random KI270728.1
chr17 17
chr17_GL000205v2_random GL000205.2
chr17_KI270729v1_random KI270729.1
chr17_KI270730v1_random KI270730.1
chr18 18
chr19 19
chr1_KI270706v1_random KI270706.1
chr1_KI270707v1_random KI270707.1
chr1_KI270708v1_random KI270708.1
chr1_KI270709v1_random KI270709.1
chr1_KI270710v1_random KI270710.1
chr1_KI270711v1_random KI270711.1
chr1_KI270712v1_random KI270712.1
chr1_KI270713v1_random KI270713.1
chr1_KI270714v1_random KI270714.1
chr2 2
chr20 20
chr21 21
chr22 22
chr22_KI270731v1_random KI270731.1
chr22_KI270732v1_random KI270732.1
chr22_KI270733v1_random KI270733.1
chr22_KI270734v1_random KI270734.1
chr22_KI270735v1_random KI270735.1
chr22_KI270736v1_random KI270736.1
chr22_KI270737v1_random KI270737.1
chr22_KI270738v1_random KI270738.1
chr22_KI270739v1_random KI270739.1
chr2_KI270715v1_random KI270715.1
chr2_KI270716v1_random KI270716.1
chr3 3
chr3_GL000221v1_random GL000221.1
chr4 4
chr4_GL000008v2_random GL000008.2
chr5 5
chr5_GL000208v1_random GL000208.1
chr6 6
chr7 7
chr8 8
chr9 9
chr9_KI270717v1_random KI270717.1
chr9_KI270718v1_random KI270718.1
chr9_KI270719v1_random KI270719.1
chr9_KI270720v1_random KI270720.1
chrM MT
chrUn_GL000195v1 GL000195.1
chrUn_GL000213v1 GL000213.1
chrUn_GL000214v1 GL000214.1
chrUn_GL000216v2 GL000216.2
chrUn_GL000218v1 GL000218.1
chrUn_GL000219v1 GL000219.1
chrUn_GL000220v1 GL000220.1
chrUn_GL000224v1 GL000224.1
chrUn_GL000226v1 GL000226.1
chrUn_KI270302v1 KI270302.1
chrUn_KI270303v1 KI270303.1
chrUn_KI270304v1 KI270304.1
chrUn_KI270305v1 KI270305.1
chrUn_KI270310v1 KI270310.1
chrUn_KI270311v1 KI270311.1
chrUn_KI270312v1 KI270312.1
chrUn_KI270315v1 KI270315.1
chrUn_KI270316v1 KI270316.1
chrUn_KI270317v1 KI270317.1
chrUn_KI270320v1 KI270320.1
chrUn_KI270322v1 KI270322.1
chrUn_KI270329v1 KI270329.1
chrUn_KI270330v1 KI270330.1
chrUn_KI270333v1 KI270333.1
chrUn_KI270334v1 KI270334.1
chrUn_KI270335v1 KI270335.1
chrUn_KI270336v1 KI270336.1
chrUn_KI270337v1 KI270337.1
chrUn_KI270338v1 KI270338.1
chrUn_KI270340v1 KI270340.1
chrUn_KI270362v1 KI270362.1
chrUn_KI270363v1 KI270363.1
chrUn_KI270364v1 KI270364.1
chrUn_KI270366v1 KI270366.1
chrUn_KI270371v1 KI270371.1
chrUn_KI270372v1 KI270372.1
chrUn_KI270373v1 KI270373.1
chrUn_KI270374v1 KI270374.1
chrUn_KI270375v1 KI270375.1
chrUn_KI270376v1 KI270376.1
chrUn_KI270378v1 KI270378.1
chrUn_KI270379v1 KI270379.1
chrUn_KI270381v1 KI270381.1
chrUn_KI270382v1 KI270382.1
chrUn_KI270383v1 KI270383.1
chrUn_KI270384v1 KI270384.1
chrUn_KI270385v1 KI270385.1
chrUn_KI270386v1 KI270386.1
chrUn_KI270387v1 KI270387.1
chrUn_KI270388v1 KI270388.1
chrUn_KI270389v1 KI270389.1
chrUn_KI270390v1 KI270390.1
chrUn_KI270391v1 KI270391.1
chrUn_KI270392v1 KI270392.1
chrUn_KI270393v1 KI270393.1
chrUn_KI270394v1 KI270394.1
chrUn_KI270395v1 KI270395.1
chrUn_KI270396v1 KI270396.1
chrUn_KI270411v1 KI270411.1
chrUn_KI270412v1 KI270412.1
chrUn_KI270414v1 KI270414.1
chrUn_KI270417v1 KI270417.1
chrUn_KI270418v1 KI270418.1
chrUn_KI270419v1 KI270419.1
chrUn_KI270420v1 KI270420.1
chrUn_KI270422v1 KI270422.1
chrUn_KI270423v1 KI270423.1
chrUn_KI270424v1 KI270424.1
chrUn_KI270425v1 KI270425.1
chrUn_KI270429v1 KI270429.1
chrUn_KI270435v1 KI270435.1
chrUn_KI270438v1 KI270438.1
chrUn_KI270442v1 KI270442.1
chrUn_KI270448v1 KI270448.1
chrUn_KI270465v1 KI270465.1
chrUn_KI270466v1 KI270466.1
chrUn_KI270467v1 KI270467.1
chrUn_KI270468v1 KI270468.1
chrUn_KI270507v1 KI270507.1
chrUn_KI270508v1 KI270508.1
chrUn_KI270509v1 KI270509.1
chrUn_KI270510v1 KI270510.1
chrUn_KI270511v1 KI270511.1
chrUn_KI270512v1 KI270512.1
chrUn_KI270515v1 KI270515.1
chrUn_KI270516v1 KI270516.1
chrUn_KI270517v1 KI270517.1
chrUn_KI270518v1 KI270518.1
chrUn_KI270519v1 KI270519.1
chrUn_KI270521v1 KI270521.1
chrUn_KI270522v1 KI270522.1
chrUn_KI270528v1 KI270528.1
chrUn_KI270529v1 KI270529.1
chrUn_KI270530v1 KI270530.1
chrUn_KI270538v1 KI270538.1
chrUn_KI270539v1 KI270539.1
chrUn_KI270544v1 KI270544.1
chrUn_KI270548v1 KI270548.1
chrUn_KI270579v1 KI270579.1
chrUn_KI270580v1 KI270580.1
chrUn_KI270581v1 KI270581.1
chrUn_KI270582v1 KI270582.1
chrUn_KI270583v1 KI270583.1
chrUn_KI270584v1 KI270584.1
chrUn_KI270587v1 KI270587.1
chrUn_KI270588v1 KI270588.1
chrUn_KI270589v1 KI270589.1
chrUn_KI270590v1 KI270590.1
chrUn_KI270591v1 KI270591.1
chrUn_KI270593v1 KI270593.1
chrUn_KI270741v1 KI270741.1
chrUn_KI270742v1 KI270742.1
chrUn_KI270743v1 KI270743.1
chrUn_KI270744v1 KI270744.1
chrUn_KI270745v1 KI270745.1
chrUn_KI270746v1 KI270746.1
chrUn_KI270747v1 KI270747.1
chrUn_KI270748v1 KI270748.1
chrUn_KI270749v1 KI270749.1
chrUn_KI270750v1 KI270750.1
chrUn_KI270751v1 KI270751.1
chrUn_KI270752v1 KI270752.1
chrUn_KI270753v1 KI270753.1
chrUn_KI270754v1 KI270754.1
chrUn_KI270755v1 KI270755.1
chrUn_KI270756v1 KI270756.1
chrUn_KI270757v1 KI270757.1
chrX X
chrY Y
chrY_KI270740v1_random KI270740.1
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