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How to merge these columns following it from SURVIVOR merge result, and gain the Paragraph software input file #212

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HuTaoJiaZiAckerman opened this issue Mar 15, 2024 · 0 comments
Open

How to merge these columns following it from SURVIVOR merge result, and gain the Paragraph software input file #212

HuTaoJiaZiAckerman opened this issue Mar 15, 2024 · 0 comments

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@HuTaoJiaZiAckerman
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Hi, developer!
I want to merge these columns:

FORMAT SRS971671 SRS971671_1 SRS971671_2 SRS971671_3
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 1/1:NA:5435:25,11:--:1740:INV:INV00000000:NA:NA:1_3-1_5438 ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 1/1:NA:5437:0,0:  :.:INV:SV_1_1:NA:NA:1_1-1_5438
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 1/1:NA:74:0,9: -:180:DEL:DEL00000008:NA:NA:1_456034-1_456108 ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 1/1:NA:79:0,9: -:396:DEL:MantaDEL_39_0_1_0_0_0:GGCTCCCTCCGCCCCCCCCCCCCTGCCCCCCGCCCCCCCCCCCCCTCCCCCCCGCACCCCCCGCATCCCTCCCCCCTGAC:GTGGTGAGCG:1_456033-1_456112 1/1:NA:134:0,0: -:.:DEL:SV_1179_1:NA:NA:1_455979-1_456113
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:4393:23,15: -:285:DEL:MantaDEL_44_0_1_0_0_0:NA:NA:1_480682-1_485075 0/1:NA:4416:0,0: -:.:DEL:SV_4_1:NA:NA:1_480660-1_485076
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:552:26,9: -:840:DEL:DEL00000018:NA:NA:1_704463-1_705015 ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:551:28,14: -:290:DEL:MantaDEL_63_0_0_0_0_0:AGGACAGGGAGGAGGGAAATGCTGCTCTGGGGACATAATTGGCATTTGTGCTTGTCTTATTCTTAACCAAGTCCGTTAAGGAAAAAGAGCCCCAAAGTACAGATTGGAGACTTGAACTCGAAATGGAAAGAACGGTGGCTTTTGAGAACTCAAAATATTTTAATTTTCTTTTAAAAACTCTAAATGCCTTAAGAAGGTGTTTAATCTGATGTTATTTATAGCCCTGAAGTGTAGGCAGTTTTGTTTGAAGTCTAACCGTGTAGAGATGCAATGGATGTAGAGTTAACACTGTTTTACCGTCCACGGGGCTCCCTGAGTGATAAAGACGCATTTTCAGACCACGAAGCTAAGGCCCAGACGCCCACCCAAAACAGAGCAACCGAGTGGCAGCAGTCCACGTGGAGCGGCTGGCTCTCCTTCGGCCCCCAGGCTGCAGAGCCCGGGTCCTCACCCCACTTGTGTGCAGCCCAGCAGCGCAAGGGCCCCGGGAGGATGAGGGTGAGGGGCGCGCTCCTTGAAGCTGCTGCCTGGGGTCCACAGCTTCCCTGCGGT:A:1_704463-1_705014 0/1:NA:549:0,0: -:.:DEL:SV_6_1:NA:NA:1_704466-1_705015
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:86:0,11: -:300:DEL:DEL00000021:NA:NA:1_886372-1_886458 0/1:NA:84:0,5: -:143:DEL:5:NA:NA:1_886373-1_886457 0/1:NA:85:12,7: -:253:DEL:MantaDEL_81_0_1_0_0_0:CCCCCAGGGCCCCGCCCCCCCACTGGGCAAAGCCGTCCTGCCTTGTCAAACACGGGTGAGACCTTGGTGCCGCCCAACCGTGAGGT:C:1_886372-1_886457 0/1:NA:84:0,0: -:.:DEL:SV_1180_1:NA:NA:1_886374-1_886458
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 1/1:NA:564:0,21: -:499:DEL:MantaDEL_149_0_0_0_1_0:AGCCCCCTCTCGCCCATTGGGCGCCGGAGGGTCCCGGCTGTGATGGTCAGACGCTCGGCGCCCTTGGCTGGACCCCCGTCGCGGGCGTCACGGGAACAGCGCGTGCAGCGAAGCAGGGAACAGCTGCCGTGTTCGCTGCCAGTGTTCGTCTCAGACACTGCGCCTGGTCCCGAGTCTCCCTACGTCTCTCAAGGGCAGTATCGTGCCATCCAAACGCTCATGTCACAACGACTTACTGACCACACGTTTGGTGCAAAGCACGTCTTCATCTTCGAGGAGCTCTCGAACGTGCCGGTGACGAGAAAGGAGCTCGGCCATGGTGCCCGACGCCGCCTCTGTGGGGGCACGGATTCTCTGCGGGTCTCCCAAGCTGGCGACTGTCACAGTGCCAGTGGAAGGACAGGACGTGTCTGAGGACACGTGTCCACTGTTCTTTCTTTGTAGAGCCACATCTGCGGCACAGGGGTCGAACACCAGATCCGAGCCACGTCTGTGACCTACACCGCATCCTGAGGCGACGCCAGAACCTTAACCCACTGAGTGAGGGCAGGGATCAAACCCGCAC:A:1_1211580-1_1212144 1/1:NA:619:0,0: -:.:DEL:SV_14_1:NA:NA:1_1211526-1_1212145
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:3060:20,8: -:840:DEL:DEL00000029:NA:NA:1_1243888-1_1246948 ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:3062:14,17: -:414:DEL:MantaDEL_146_0_1_0_0_0:NA:NA:1_1243885-1_1246947 0/1:NA:3105:0,0: -:.:DEL:SV_15_1:NA:NA:1_1243843-1_1246948
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:648:24,8: -:1020:DEL:DEL00000030:NA:NA:1_1302074-1_1302722 ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:647:13,15: -:386:DEL:MantaDEL_157_0_0_0_0_0:GATGGGTTCCGGGCCAGTAGAATTTATTCTCCTGCGAACGGAAACGCTGGAGCTTTTGTTTTAAATGCAATTGAGTTTTCCAGTTTCGACAGAGAAGGCCCTGTGTTTGCCTCCACGAGAAATGTTCTCATCGAATACAACCTGCACCTTTTCACGCACAAGAGAAGCACGGGAGAGACATCGGTTTGTTTAAATACATTCACTGATGATTCCAGAAGCAGATTCAATATGAGACTTAAAATTCAAAGCGATCGATTAGCTAAGAGGGATTCAAGAAACCAGATGACCCACTTCTAAGGTGGACATGAGGTCACGACAGGAAGAGGGCTGAGGAGAACGCGGGGGTGCCCTAGAGGGCTAGGCGCAGGGTTCCAACCTCCTGGCAGAATAAGATCACAGCTAAGTAAATTCAGCCCGCTTCCCCGCCTCCACGTCCGTCAGATAACATTAAAACATTCCTACAGCAGGGAATTCGTGTTCGCGTTCATTAAGTATTCTGCGGCGATTCGCAATAATAATTTTAACCTTTAGATGGTCACTTAAAGCTCTGCCTGATGCCGGTGGAAGTGGTCCACGAGCATCCAGGGCTAACTGACCTTATCCCCACAGACATGTGCTGCGGGCAAGGTCATCACAAGACTCTGAACC:G:1_1302074-1_1302721 0/1:NA:675:0,0: -:.:DEL:SV_16_1:NA:NA:1_1302047-1_1302722
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:1890:23,15: -:264:DEL:MantaDEL_192_0_1_0_0_0:NA:NA:1_1655388-1_1657278 0/1:NA:1913:0,0: -:.:DEL:SV_17_1:NA:NA:1_1655393-1_1657306
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:308:8,13: -:132:DEL:MantaDEL_234_0_0_0_1_1:CGCCCTGTTTTATTTTATTTTTTTTGTCTTTTGTCTTTTTTTGTTGTTGTTGTTGTTGTTGTTGCTATTTCTTGGGCCGCTCCCGCGACATATGGAGGTTCCCAGGCCAGGGGTCGAATCGGAGCTGTAGCCACCAGCCTACGCCAGAGCCACAGCAACGCGGGATCCGAGCTGCGTCTGCAATGCACACCACAACTCACGGCAACGCCGGATCGTTAACCCACTGAGCAAGGGCAGGGACCGAACCTGCAACCTCATGGTTCCTAGTCAGATTCGTTAACCACTGCGCCACGACGGGAACTCCTGACG:CA:1_1842609-1_1842917 0/1:NA:514:0,0: -:.:DEL:SV_18_1:NA:NA:1_1842620-1_1843134
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:337:0,9: -:240:DEL:DEL00000040:NA:NA:1_2662701-1_2663038 0/1:NA:322:0,5: -:200:DEL:15:NA:NA:1_2662715-1_2663037 0/1:NA:336:20,8: -:117:DEL:MantaDEL_314_0_1_0_0_0:TCCACCCATCTTTTATTTTTTTTAATTTTTTTTAATTTTTTATTTTTTTTGTCTTTTGTCTTTTTTGTTGTTGTTGTTGTTGCTGTTGTTATTGTTGCTATTTCTTGGGCCGCTCCCGCGGCACATGGAGGTTCCCAGGCTAGGGGTCGAATCGGAGCTGTAGCCACCAGCCTACGCCAGAGCCACAGCAACGCAGGATCCGAGCCGCGTCTGCAACCTACACCACAGCTCACGGCAACGCCGGATCGTTAACCCACTGAGCAAGGCCAGGGATCGAATCCGCAACCTCATGGTTCCTAGTCGGATTCGTTAACCACTGCGCCACGACGGGAACTCC:T:1_2662701-1_2663037 0/1:NA:687:0,0: -:.,.:DEL,DEL:SV_1181_1:NA:NA:1_2662360-1_2663047,1_2662716-1_2663038
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:885:20,12: -:840:DEL:DEL00000041:NA:NA:1_2836980-1_2837865 0/1:NA:883:0,13: -:335:DEL:16:NA:NA:1_2836981-1_2837864 0/1:NA:884:24,15: -:415:DEL:MantaDEL_342_0_1_0_0_0:CGAATCTGGCTAGGAACCATGAGGGTGCGGTTTCGATCCCTGGCCTTGCTCCGGGGTTAAGGAGATCTGGTGTTGCTGTGGCTGTGGTGTAGGCCAGCAGCTGAAGCTCCGATTGGACCCCTGGCCTGGGAATCTCCATGTGCCTCCGGTGCGGCCCTGGAAGGGAAAAAAAAAAAAACACACACAAAACCCAAAAAATACAGCATCGTATATTATAAAAATAGCTTTCCTTAGGACTAAATTGCCTCTAAGGTACTAATGCGTGGTACTAGTGTGAGAGAAAAGTAGAAACAGCTTCCTTTCTCCCAGTTTTTATTTTGAAAAGTATCCCATCTACAGAAAAGCTGCAGGATTCGTACGAGATGAGCTGCTGTCCTCTTCACCTAAATCTCCCATGTGCCCAATGGGCTGCAGGGCCTGACTCCGTTTCGGATGTTTGGCCGCTGGCAGCTTTCGGATCCCGCCACCCAGCTTCCCTTCTGCTCCAGACCTGGGCAAGCTAGCCGAACAGGCCACATGGCCCTTCCCTCAGTGCCAGTGAGCGCTCAGGCCACCCAAGCCCTGACCCTACCTGAGAACCCCCTAGCACCCCGAGAACCACACTGACACCCCCACCTGTTGGCTCTCAGGCCATTTTCAGGCCTACTGGGGCCCGGCCCTGCTCCCCGGAAAGCCTCCTATGTGAGTGATAAATCATCCCACACCCACTTGATGTGCGCGTGGGCTTTGCAGCCTCAGTACCTGAACCAGGGCTTGGATGGGAGGTCCATCTCGCTCCCGAGTGATGGACAAGCATTTGCCTACGTTTTCTCCTCCTCTCCCCCAACCCCTCTTCTTTCCCTCACAACAATGGTTATTTTTGGCCGAACCCCTTGAGAGTCATTT:C:1_2836980-1_2837864 0/1:NA:955:0,0: -:.:DEL:SV_23_1:NA:NA:1_2836910-1_2837865
GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/1:NA:857:24,9: -:883:DEL:DEL00000045:NA:NA:1_3101792-1_3102649 ./.:NaN:0:0,0:--:NaN:NaN:NaN:NAN:NAN:NAN 0/1:NA:856:23,13: -:264:DEL:MantaDEL_358_0_1_0_0_0:CCGCGTTGGTGGCGCCCCACCCAAAGATCTTCGGCGGGTCCTAAATCAGTCCGTTGTGTTCGTGCTGTGTCCTCCACCTGCCCCTGGAGAATGGGTATCGATGCTCTGATAAGCCCGATAAGCGACGCTTTAGCGTTACTGTCTCCTCCTCCGTCTCCCTTCTTTTCCGCCCTCCGTGCGTTCAGCAAATGGTCTTGTGAACAAGTGCTACGACCTGCTGGGAGGCTAAGTGTCAGGTGCGGTGACCCCCACAGACCAGGTCTCTGCCCAGCTTTTACATTCTTGGGGGTGGGGGATGGTGGTGAGGAGGGAGGAGAGAAGCAAACGGCCCGTTTAAGACACGTGCCCAAATGGGGACAACGCAGGTGTTTGCGGGAGTACACGGGAGGGCTCCGAACTCAGACCTGAAGGTGCAGGCGCAGCTCACCAGATGCAGTGATGTGCCGCCTGACGTCCGCCAGACTCCAGACTGGCTGGTGATCTTCATGCTCCCAGGTGATGGCAAATACAGGGTTTAATACATTTGGATGCTTTAATAGATTGGTGGAAAATCAGCAAGTCAAAAATTAGATCGGGAGTTCTCGTCGTGGCGCAGTGGTTAACAAATCCGACTGGGAACCATGAGGTTGCGGGTTCGGTCCCTGCCCTTGCTCAGTGGGTTAACGATCCGGCGTTGCCGAGAGCTGTGGTGTAGGTTGCAGACGCGACTCGGATCCCGCGTTGCTGTGGCTCTGGCGTAGGCCGGTGGCTACAGCTCCGATTCCACCCCTAGCCTGGGAACCTCCATATGCCACGAGAGCGGCCCAAAGAAATAGCAAAAAGACAAAAAAAAAAAAAAAAAAATTAGATCGAAGACA:C:1_3101792-1_3102648 0/1:NA:856:0,0: -:.:DEL:SV_25_1:NA:NA:1_3101793-1_3102649

This is filter result using SURVIVOR filter (SURVIVOR filter SRS971671.merge.vcf NA 50 100000 0 -1 SRS971671.filter.vcf).
Obviously! These columns is same sample, just only use different methods, such as manta, delly, tiddit, and lumpy.
So, I want merge it enable become a column.
Could you tell any approachs? Thanks!
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