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We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 10 columns, instead of 13 in line 1.
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21 lines (21 loc) · 8 KB
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#CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT,SRR8707685
chr13,16226824,.,G,C,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16226824|16226824|IGR||SNP|G|G|C|g.chr13:16226824G>C|no_transcript|||||||0.36159600997506236|GAAGAATTCTGAGAAACTTCT|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=55.00;QD=25.36;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16226827,.,A,T,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16226827|16226827|IGR||SNP|A|A|T|g.chr13:16226827A>T|no_transcript|||||||0.36159600997506236|GAATTCTGAGAAACTTCTTTG|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=55.00;QD=28.73;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16226833,.,C,A,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16226833|16226833|IGR||SNP|C|C|A|g.chr13:16226833C>A|no_transcript|||||||0.3640897755610973|TGAGAAACTTCTTTGTGATGT|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=55.00;QD=30.97;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16226840,.,A,G,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16226840|16226840|IGR||SNP|A|A|G|g.chr13:16226840A>G|no_transcript|||||||0.3640897755610973|CTTCTTTGTGATGTGTGCATT|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=55.00;QD=27.24;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16226847,.,C,T,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16226847|16226847|IGR||SNP|C|C|T|g.chr13:16226847C>T|no_transcript|||||||0.3566084788029925|GTGATGTGTGCATTCATCTCA|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=55.00;QD=28.20;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16564887,.,A,T,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16564887|16564887|IGR||SNP|A|A|T|g.chr13:16564887A>T|no_transcript|||||||0.3940149625935162|AAACACTCTTATTGTAGCATG|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=48.00;QD=27.51;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16564894,.,C,T,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16564894|16564894|IGR||SNP|C|C|T|g.chr13:16564894C>T|no_transcript|||||||0.4014962593516209|CTTATTGTAGCATGTGCAAGT|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=48.00;QD=29.11;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16564897,.,G,C,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16564897|16564897|IGR||SNP|G|G|C|g.chr13:16564897G>C|no_transcript|||||||0.4014962593516209|ATTGTAGCATGTGCAAGTGGA|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=48.00;QD=28.08;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16564900,.,C,G,35.48,PASS,AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16564900|16564900|IGR||SNP|C|C|G|g.chr13:16564900C>G|no_transcript|||||||0.39650872817955113|GTAGCATGTGCAAGTGGACAT|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=48.00;QD=23.23;SOR=1.609,GT:AD:DP:FT:GQ:PL,1/1:0,1:1:DP_filter;GQ_filter:3:45,3,0
chr13,16692648,.,T,TTC,78.28,PASS,AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[Unknown|hg38|chr13|16692648|16692649|IGR||INS|-|-|TC|g.chr13:16692648_16692649insTC|no_transcript|||||||0.38|AGTGAACATTAGGAGAGCTT|||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=38.00;QD=28.55;SOR=0.693,GT:AD:DP:FT:GQ:PL,1/1:0,2:2:DP_filter;GQ_filter:6:90,6,0
chr17,83232592,.,A,G,121.84,PASS,AC=2;AF=1.00;AN=2;DP=3;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83232592|83232592|RNA||SNP|A|A|G|g.chr17:83232592A>G|ENST00000425566.1|+|||c.e3+2698A>G|||0.49875311720698257|GTGAGGAAAAACTTCCTGTCT|ENSG00000262094_ENST00000570366.1_FIVE_PRIME_FLANK/ENSG00000262094_ENST00000575205.1_FIVE_PRIME_FLANK||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=60.00;QD=30.10;SOR=1.179,GT:AD:DP:FT:GQ:PL,1/1:0,3:3:DP_filter;GQ_filter:9:135,9,0
chr17,83240053,.,T,C,61.64,PASS,AC=1;AF=0.500;AN=2;BaseQRankSum=-0.319;DP=4;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240053|83240053|RNA||SNP|T|T|C|g.chr17:83240053T>C|ENST00000573039.1|+|||c.e1+127T>C|||0.47880299251870323|CGCATGTCACTCACCTTCAGG|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=48.81;MQRankSum=-0.674;QD=15.41;ReadPosRankSum=-0.319;SOR=0.446,GT:AD:DP:FT:GQ:PL,0/1:1,3:4:DP_filter:30:69,0,30
chr17,83240114,.,T,C,255.97,PASS,AC=2;AF=1.00;AN=2;DP=6;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240114|83240114|RNA||SNP|T|T|C|g.chr17:83240114T>C|ENST00000573039.1|+|||c.e1+188T>C|||0.516209476309227|CTCGGAAGAGTACCCCCACGA|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=2;MLEAF=1.00;MQ=41.58;QD=27.18;SOR=1.329,GT:AD:DP:FT:GQ:PL,1/1:0,6:6:DP_filter:18:270,18,0
chr17,83240122,.,C,G,416.06,PASS,AC=2;AF=1.00;AN=2;DP=10;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240122|83240122|RNA||SNP|C|C|G|g.chr17:83240122C>G|ENST00000573039.1|+|||c.e1+196C>G|||0.516209476309227|AGTACCCCCACGAGAAACAAG|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=2;MLEAF=1.00;MQ=42.11;QD=32.00;SOR=1.609,GT:AD:DP:GQ:PL,1/1:0,10:10:30:430,30,0
chr17,83240166,.,G,A,751.06,PASS,AC=2;AF=1.00;AN=2;DP=20;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240166|83240166|RNA||SNP|G|G|A|g.chr17:83240166G>A|ENST00000573039.1|+|||c.e1-225G>A|||0.5012468827930174|GTTTCCGCTGGCCACTGAGTC|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=2;MLEAF=1.00;MQ=45.95;QD=28.71;SOR=1.292,GT:AD:DP:GQ:PL,1/1:0,19:19:57:765,57,0
chr17,83240181,.,GT,G,211.60,PASS,AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=22;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240182|83240182|RNA||DEL|T|T|-|g.chr17:83240182delT|ENST00000573039.1|+|||c.e1-210GT>G|||0.4912718204488778|GAGTCGGCCGTGAAGAAGATA|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=46.05;MQRankSum=-0.195;QD=10.08;ReadPosRankSum=-1.084;SOR=0.665,GT:AD:DP:GQ:PL,0/1:14,7:21:99:219,0,530
chr17,83240206,.,C,T,68.64,PASS,AC=1;AF=0.500;AN=2;BaseQRankSum=-0.621;DP=28;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240206|83240206|RNA||SNP|C|C|T|g.chr17:83240206C>T|ENST00000573039.1|+|||c.e1-185C>T|||0.4937655860349127|GAAAACAACACGCTTGTGTTC|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=45.11;MQRankSum=0.431;QD=2.64;ReadPosRankSum=0.426;SOR=0.392,GT:AD:DP:GQ:PL,0/1:20,6:26:76:76,0,600
chr17,83240268,.,G,C,590.06,PASS,AC=2;AF=1.00;AN=2;DP=25;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240268|83240268|RNA||SNP|G|G|C|g.chr17:83240268G>C|ENST00000573039.1|+|||c.e1-123G>C|||0.44389027431421446|TGTGAAGAAGGTCTATGACAG|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=2;MLEAF=1.00;MQ=46.60;QD=26.82;SOR=1.085,GT:AD:DP:GQ:PL,1/1:0,22:22:66:604,66,0
chr17,83240319,.,GAGA,G,220.60,PASS,AC=1;AF=0.500;AN=2;BaseQRankSum=-2.198;DP=15;ExcessHet=0.0000;FS=2.363;FUNCOTATION=[RPL23AP87|hg38|chr17|83240320|83240322|RNA||DEL|AGA|AGA|-|g.chr17:83240320_83240322delAGA|ENST00000573039.1|+|||c.e1-72GAGA>G|||0.3920595533498759|CCTGATAAAGAGAAGAAGGCATA|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=51.70;MQRankSum=1.364;QD=15.76;ReadPosRankSum=0.125;SOR=0.169,GT:AD:DP:GQ:PL,0/1:8,6:14:99:228,0,298
chr17,83240324,.,G,C,95.64,PASS,AC=1;AF=0.500;AN=2;BaseQRankSum=0.221;DP=14;ExcessHet=0.0000;FS=0.000;FUNCOTATION=[RPL23AP87|hg38|chr17|83240324|83240324|RNA||SNP|G|G|C|g.chr17:83240324G>C|ENST00000573039.1|+|||c.e1-67G>C|||0.3865336658354115|ATAAAGAGAAGAAGGCATATG|RPL23AP87_ENST00000425566.1_RNA||||||||||||||||||||||||||||false||];MLEAC=1;MLEAF=0.500;MQ=52.02;MQRankSum=-2.674;QD=6.83;ReadPosRankSum=-0.976;SOR=0.458,GT:AD:DP:GQ:PL,0/1:9,5:14:99:103,0,363