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macarthur-lab / gnomad_browser

gnomAD browser pre-ASHG 2018
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"precalculate_metrics" function fails due to string values which cannot be converted to float #57

Closed nabramovs closed 6 years ago

nabramovs commented 7 years ago

"AS_RF" and "AB_MEDIAN" metrics (in variant["quality_metrics"]) have dot values (".") in several variants, consequently "precalculate_metrics" function fails to convert them to float (exac.py line 561):

metrics[metric].append(float(value))

I fixed this by adding: 

if value == '.':
    value = 0

before converting string to float.

However, a proper fix requires updating VCF files. Here are 2 lists of variants in csv format which metrics has to be fixed in exomes and genomes (coding only) VCF files:

Exomes

variant_id,xpos,metric 3-1425118-C-CTTATGAATGTGCCAATGGACTTCGCAATAGCTCCTATTCAACAGTCCTATCCTACTAGCCTGTTGTTAGCATATGATA,3001425118,AS_RF 3-1425118-C-CTTATGAATGTGCCAATGGACTTCGCAATAGCTCCTATTCAACAGTCCTATCCTACTAGCCTGTTGTTAGCATATGATA,3001425118,AB_MEDIAN 1-1246148-T-TGGGCGGCTCTGGGTCACAGGTACGGAGGATGACGGCTGTGCTGGTGGGTCAC,1001246148,AS_RF 1-1246148-T-TGGGCGGCTCTGGGTCACAGGTACGGAGGATGACGGCTGTGCTGGTGGGTCAC,1001246148,AB_MEDIAN 4-1388593-A-ACACGTGCCCATGTGGAGTGCCCGCCTGCT,4001388593,AS_RF 4-1388593-A-ACACGTGCCCATGTGGAGTGCCCGCCTGCT,4001388593,AB_MEDIAN 7-16128791-A-ATATATACGTACGTATATACATATATGTGTG,7016128791,AS_RF 7-16128791-A-ATATATACGTACGTATATACATATATGTGTG,7016128791,AB_MEDIAN 5-41475846-T-TCTGTTACTACTTGAGACCATCATTACAGCAGTTACTG,5041475846,AS_RF 5-41475846-T-TCTGTTACTACTTGAGACCATCATTACAGCAGTTACTG,5041475846,AB_MEDIAN 6-30995807-T-TCAGCCTCTACTACAGGCTCTGAGACCACCA,6030995807,AS_RF 6-30995807-T-TCAGCCTCTACTACAGGCTCTGAGACCACCA,6030995807,AB_MEDIAN 4-71024425-C-CCCTGTTGCAGCTGAGCCTGCTGCAGAGGCACCTGTTGGAGCTGAGCCTGCTGCAGAGGCA,4071024425,AS_RF 4-71024425-C-CCCTGTTGCAGCTGAGCCTGCTGCAGAGGCACCTGTTGGAGCTGAGCCTGCTGCAGAGGCA,4071024425,AB_MEDIAN 7-63726864-A-AACCACAAGAGAATTCATACTGGAGAGAAACCATACACATGTGAAGAATGTGGCAAAGCCTTTAGCTTATCCTCATCCCTCACTT,7063726864,AS_RF 7-63726864-A-AACCACAAGAGAATTCATACTGGAGAGAAACCATACACATGTGAAGAATGTGGCAAAGCCTTTAGCTTATCCTCATCCCTCACTT,7063726864,AB_MEDIAN 6-39025360-G-GCCCCCTCCCCGACCTGGTACCTGCCCTGGGCCAGCAGTGGTGAA,6039025360,AS_RF 6-39025360-G-GCCCCCTCCCCGACCTGGTACCTGCCCTGGGCCAGCAGTGGTGAA,6039025360,AB_MEDIAN 4-87811357-AGGG-A,4087811357,AS_RF 4-87811357-AGGG-A,4087811357,AB_MEDIAN 1-26671505-A-C,1026671505,AS_RF 1-26671505-A-C,1026671505,AB_MEDIAN 8-98788165-C-CGGGCTCCAGGCGA,8098788165,AS_RF 8-98788165-C-CGGGCTCCAGGCGA,8098788165,AB_MEDIAN 7-100349865-T-TCCCCAGAAAAACCCACCATCCCCACAGAAAAACCCACCATCCCCACAGAAAAACCCACCATCC,7100349865,AS_RF 7-100349865-T-TCCCCAGAAAAACCCACCATCCCCACAGAAAAACCCACCATCCCCACAGAAAAACCCACCATCC,7100349865,AB_MEDIAN 8-144641091-C-CGACACTCTGGCTGGGTTTTGCAGTGGGTCCCTGGT,8144641091,AS_RF 8-144641091-C-CGACACTCTGGCTGGGTTTTGCAGTGGGTCCCTGGT,8144641091,AB_MEDIAN 1-53925395-T-TC,1053925395,AS_RF 1-53925395-T-TC,1053925395,AB_MEDIAN 16-460351-A-ATGAGAAGTTCTTCCGGGTGGGTGCCTCGTGCGCTCTG,16000460351,AS_RF 16-460351-A-ATGAGAAGTTCTTCCGGGTGGGTGCCTCGTGCGCTCTG,16000460351,AB_MEDIAN 7-142494026-CAGGG-C,7142494026,AS_RF 7-142494026-CAGGG-C,7142494026,AB_MEDIAN 16-845379-C-CCTGCCCCCGGCCCCGTGCCCGCCCCCCTGTGCTGCCCGTGTGG,16000845379,AS_RF 16-845379-C-CCTGCCCCCGGCCCCGTGCCCGCCCCCCTGTGCTGCCCGTGTGG,16000845379,AB_MEDIAN 16-1031339-AGAGAGAGAGTGT-A,16001031339,AS_RF 16-1031339-AGAGAGAGAGTGT-A,16001031339,AB_MEDIAN 16-2059698-T-G,16002059698,AS_RF 16-2059698-T-G,16002059698,AB_MEDIAN 15-20739994-CCTTCTCCTCCTGCTCCCGTATCTTCTCCTCCTGCCTCCACATCTTATCCTCCTGCTCCTGCCTCTTCTCCTCCTCCCATATCTTCTCCTGCTCATGCATCTTCTCTTCCTCCCTCCACATCTCCTCCTGCTCCCGTATCTTCTCCTCCTGCCTCCACAT-C,15020739994,AS_RF 15-20739994-CCTTCTCCTCCTGCTCCCGTATCTTCTCCTCCTGCCTCCACATCTTATCCTCCTGCTCCTGCCTCTTCTCCTCCTCCCATATCTTCTCCTGCTCATGCATCTTCTCTTCCTCCCTCCACATCTCCTCCTGCTCCCGTATCTTCTCCTCCTGCCTCCACAT-C,15020739994,AB_MEDIAN 1-145328385-GGACCAAGAAGAGGAAGAAGACGAA-G,1145328385,AS_RF 1-145328385-GGACCAAGAAGAGGAAGAAGACGAA-G,1145328385,AB_MEDIAN 1-145328401-G-GAA,1145328401,AS_RF 1-145328401-G-GAA,1145328401,AB_MEDIAN 1-145328405-A-AAGG,1145328405,AS_RF 1-145328405-A-AAGG,1145328405,AB_MEDIAN 12-50746022-C-CAGAGGGATCCCCAGGGCCTGGGCCTGCTGAGGGGTGAGAGGGATCCCCAATTCCTGAGCCTGCTGAGGGGTG,12050746022,AS_RF 12-50746022-C-CAGAGGGATCCCCAGGGCCTGGGCCTGCTGAGGGGTGAGAGGGATCCCCAATTCCTGAGCCTGCTGAGGGGTG,12050746022,AB_MEDIAN 3-195452506-C-CCCGGGA,3195452506,AS_RF 3-195452506-C-CCCGGGA,3195452506,DP_MEDIAN 3-195505960-G-GTGACAGGAAGAGAGGTGGTGTGACCTGAGGATGCTGAGGAAGGGATGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTCGC,3195505960,AS_RF 3-195505960-G-GTGACAGGAAGAGAGGTGGTGTGACCTGAGGATGCTGAGGAAGGGATGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTCGC,3195505960,AB_MEDIAN 3-195507125-G-T,3195507125,AS_RF 3-195507125-G-T,3195507125,AB_MEDIAN 3-195507945-G-T,3195507945,AS_RF 3-195507945-G-T,3195507945,AB_MEDIAN 3-195509174-T-TGGTGACAGGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGTGTC,3195509174,AS_RF 3-195509174-T-TGGTGACAGGAAGAGGGGTGGCGTGACCTGTGGATGCTGAGGAAGTGTC,3195509174,AB_MEDIAN 3-195512487-G-A,3195512487,AS_RF 3-195512487-G-A,3195512487,AB_MEDIAN 13-114325990-T-TGGGAGGGATGAGGGCTACGAGGAGGGC,13114325990,AS_RF 13-114325990-T-TGGGAGGGATGA,13114325990,AS_RF 13-114325990-T-TGGGA,13114325990,AS_RF 13-114325991-G-GGGAGGGATGAGGGCTACGAGGAGGGCGGGGCGCAGCTTCCTTGGGGGTCTCTGCACAACCTCACGAGGGCTGACGGCTGTGTGGACGGTGGGGGTTCATGAGGGCTGACGGCTTCGTGGACGGTGGAGGTGTCATCGGGCACCAGGAGTCACAGGAGTGAGTGCAGGGGTCTGC,13114325991,AS_RF 13-114325991-G-GGGAGGGATGAGGGCTACGAGGA,13114325991,AS_RF 13-114325991-G-GGGAGGGATGAGGGCTACGAGGAGGGC,13114325991,AS_RF 13-114325992-G-GGAGGGATGAGGGCTACGAGGAGGGCGGGGCGCAGCTTCCTT,13114325992,AS_RF 13-114325992-G-GGAGGGATGA,13114325992,AS_RF 13-115047301-A-AAGAGGACGGCCCTGAGCAAGGTGGGGACGGGGGCGGGGCGCGCAAACCTCGCGAGG,13115047301,AS_RF 13-115047301-A-AAGAGGACGGCCCTGAGCAAGGTGGGGACGGGGGCGGGGCGCGCAAACCTCGCGAGG,13115047301,AB_MEDIAN 21-11085739-C-T,21011085739,AS_RF 21-11085739-C-T,21011085739,AB_MEDIAN 1-152084549-G-GCTGCTCGCGCCTCAGCTGCTGCTCGCGCCTCTCCTCCTCCTGCTCGCGCCTCTCCTCCTC,1152084549,AS_RF 1-152084549-G-GCTGCTCGCGCCTCAGCTGCTGCTCGCGCCTCTCCTCCTCCTGCTCGCGCCTCTCCTCCTC,1152084549,AB_MEDIAN 11-499638-C-CCCCAGCATCATGGGGAGAGGAGAGCACCACAAGGCCCCAGACCCAGCATCATGGGGAAAGGAGAGCACCACAAGGCCCCAGACCCAGCATCATGGGGAAAGGAGAGCACCACAAGGCCCCAGA,11000499638,AS_RF 11-499638-C-CCCCAGCATCATGGGGAGAGGAGAGCACCACAAGGCCCCAGACCCAGCATCATGGGGAAAGGAGAGCACCACAAGGCCCCAGACCCAGCATCATGGGGAAAGGAGAGCACCACAAGGCCCCAGA,11000499638,AB_MEDIAN 1-153043360-CGTGGG-C,1153043360,AS_RF 1-153043360-CGTGGG-C,1153043360,AB_MEDIAN 16-20499816-C-CAGAGAG,16020499816,AS_RF 16-20499816-C-CAGAGAG,16020499816,AB_MEDIAN 11-800459-A-ACAGGGGTGGGCTGAGCAAGGAGGGCTCGGGGAGGACGGTAAGGCTCCCCCTCCAGGGCAGGGAGGGCCTATCAGCATCCACGCAGTCAGGGCAATCCAGGGGG,11000800459,AS_RF 11-800459-A-ACAGGGGTGGGCTGAGCAAGGAGGGCTCGGGGAGGACGGTAAGGCTCCCCCTCCAGGGCAGGGAGGGCCTATCAGCATCCACGCAGTCAGGGCAATCCAGGGGG,11000800459,AB_MEDIAN 11-1457405-T-TGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG,11001457405,AS_RF 11-1457405-T-TGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG,11001457405,DP_MEDIAN 2-233273125-GT-G,2233273125,AS_RF 2-233273125-GT-G,2233273125,DP_MEDIAN 2-233273130-T-A,2233273130,AS_RF 2-233273130-T-A,2233273130,DP_MEDIAN 14-73730532-C-CT,14073730532,AS_RF 14-73730532-C-CT,14073730532,AB_MEDIAN 2-241991904-T-TCAAGCAGGGTACATGGGATACCAGTGCCAGGCAGGTGAGATGGCCAGGGCC,2241991904,AS_RF 2-241991904-T-TCAAGCAGGGTACATGGGATACCAGTGCCAGGCAGGTGAGATGGCCAGGGCC,2241991904,AB_MEDIAN 11-10823575-G-GCACACTCCTAAAATAGTTTCATGTTTTAATAGCAAATGAAATCACATATATTGCAGAATTTAACATTTGTTGCCTA,11010823575,AS_RF 11-10823575-G-GCACACTCCTAAAATAGTTTCATGTTTTAATAGCAAATGAAATCACATATATTGCAGAATTTAACATTTGTTGCCTA,11010823575,AB_MEDIAN 2-242695022-A-AGGGTTGGAGCCACACCTGGTCTGGGGCATTCGCTGTCCTGGGTCAGAGCCCCTCCTGGTCTGGGACATTCGCTGTCTG,2242695022,AS_RF 2-242695022-A-AGGGTTGGAGCCACACCTGGTCTGGGGCATTCGCTGTCCTGGGTCAGAGCCCCTCCTGGTCTGGGACATTCGCTGTCTG,2242695022,AB_MEDIAN 10-5958437-T-TGAAGTGTTAGGGATCTGAGGATGGGGGAACAGGGGAAGTGTTAGGGATCTGAGGATGGGGAAACAGGG,10005958437,AS_RF 10-5958437-T-TGAAGTGTTAGGGATCTGAGGATGGGGGAACAGGGGAAGTGTTAGGGATCTGAGGATGGGGAAACAGGG,10005958437,AB_MEDIAN 10-7622053-T-A,10007622053,AS_RF 10-7622053-T-A,10007622053,DP_MEDIAN 15-82808379-C-CGTGAACAGGAGGAGAGGCTGT,15082808379,AS_RF 15-82808379-C-CGTGAACAGGAGGAGAGGCTGT,15082808379,AB_MEDIAN 1-186276876-C-CACCCCTAAGGAGCCTGCTCCAACT,1186276876,AS_RF 1-186276876-C-CACCCCTAAGGAGCCTGCTCCAACT,1186276876,AB_MEDIAN 14-105063463-A-AGCTGCAGCCAGAAACAGGAGGGGCAGGCTCACTGGACACCACCTCCCAGGCGACCCCCGCCCCCAG,14105063463,AS_RF 14-105063463-A-AGCTGCAGCCAGAAACAGGAGGGGCAGGCTCACTGGACACCACCTCCCAGGCGACCCCCGCCCCCAG,14105063463,AB_MEDIAN 14-106330484-A-T,14106330484,AS_RF 14-106330484-A-T,14106330484,AB_MEDIAN 16-70010458-G-GAGGGGCAAGGAGACACTCCTTGAGATTATCATCCACTGAGGGTGGAAGAGGAGAGGGTGGAAGAGGAGCAAGAGGACACTCCTTGATATTATCATCCACTGAGGGTGGAA,16070010458,AS_RF 16-70010458-G-GAGGGGCAAGGAGACACTCCTTGAGATTATCATCCACTGAGGGTGGAAGAGGAGAGGGTGGAAGAGGAGCAAGAGGACACTCCTTGATATTATCATCCACTGAGGGTGGAA,16070010458,DP_MEDIAN 16-70023904-GAGCCAAAAGCGC-G,16070023904,AS_RF 16-70023904-GAGCCAAAAGCGC-G,16070023904,AB_MEDIAN X-3030576-G-GGGTCCTAACGAGAAGAGATAATTACAATCAGGCTACCAGAGGAAGCCTTT,23003030576,AS_RF X-3030576-G-GGGTCCTAACGAGAAGAGATAATTACAATCAGGCTACCAGAGGAAGCCTTT,23003030576,AB_MEDIAN 10-73056496-A-AGAGGTGAGGGAAGTCGGGGCCACATATTCCAGCTGCACACCACACTGGCG,10073056496,AS_RF 10-73056496-A-AGAGGTGAGGGAAGTCGGGGCCACATATTCCAGCTGCACACCACACTGGCG,10073056496,AB_MEDIAN 12-124383357-T-TGTAGGTGAGTGAGGGCGGGGCCAGGGCAGCCCATCCCCAACACCCAATACCCACC,12124383357,AS_RF 12-124383357-T-TGTAGGTGAGTGAGGGCGGGGCCAGGGCAGCCCATCCCCAACACCCAATACCCACC,12124383357,AB_MEDIAN X-34148805-C-CGAGACTGGACGTCCGACGAGTCTTGGGAGGCTCCGAGCG,23034148805,AS_RF X-34148805-C-CGAGACTGGACGTCCGACGAGTCTTGGGAGGCTCCGAGCG,23034148805,AB_MEDIAN 12-132516666-G-GGGAGATGCAAAGACATCCACATATACAGGTGAGGGCCTGCGGGGGATAGGATCA,12132516666,AS_RF 12-132516666-G-GGGAGATGCAAAGACATCCACATATACAGGTGAGGGCCTGCGGGGGATAGGATCA,12132516666,AB_MEDIAN 12-132811406-A-AGCTGTGGGCTCCGTGCGTGGCCCCGGGGCTCG,12132811406,AS_RF 12-132811406-A-AGCTGTGGGCTCCGTGCGTGGCCCCGGGGCTCG,12132811406,AB_MEDIAN 12-133084970-G-T,12133084970,AS_RF 12-133084970-G-T,12133084970,DP_MEDIAN 10-95107330-A-AAAAT,10095107330,AS_RF 10-95107330-A-AAAAT,10095107330,AB_MEDIAN 16-89017349-G-GTCCCCTGGACCGGCACCGCCACAGAGGGTCAGAGTGTTGGCACCTGTCTTCCGGATCTGTTCACCCC,16089017349,AS_RF 16-89017349-G-GTCCCCTGGACCGGCACCGCCACAGAGGGTCAGAGTGTTGGCACCTGTCTTCCGGATCTGTTCACCCC,16089017349,AB_MEDIAN 16-89211591-C-CGGCCAGTTAACCAGAGCCCCTTTTCCTCAGGGGACACCGTGGTGTTTAAGGAT,16089211591,AS_RF 16-89211591-C-CGGCCAGTTAACCAGAGCCCCTTTTCCTCAGGGGACACCGTGGTGTTTAAGGAT,16089211591,AB_MEDIAN 16-89300159-A-ACTCGCACTGCGTATGCAACTCAACTCGCACTGCGTATGCAACTCAG,16089300159,AS_RF 16-89300159-A-ACTCGCACTGCGTATGCAACTCAACTCGCACTGCGTATGCAACTCAG,16089300159,AB_MEDIAN 20-35154222-G-GCTGGCCCCACTGATCCCCATCTGGCCCACAGAACCCTGATGCCAACCCACGCCCCACAGCCCAGGACCTGGCAGGGTTCTGGGAC,20035154222,AS_RF 20-35154222-G-GCTGGCCCCACTGATCCCCATCTGGCCCACAGAACCCTGATGCCAACCCACGCCCCACAGCCCAGGACCTGGCAGGGTTCTGGGAC,20035154222,AB_MEDIAN 22-45723960-G-GCGGGAGGCCTTTGGCCGGCGGCAGAACAAGCCCATGGAGTCCCTGGACTTGAAGGACAAGACCAAGGTATGGGCTGGGGGTA,22045723960,AS_RF 22-45723960-G-GCGGGAGGCCTTTGGCCGGCGGCAGAACAAGCCCATGGAGTCCCTGGACTTGAAGGACAAGACCAAGGTATGGGCTGGGGGTA,22045723960,AB_MEDIAN 10-134169436-G-GGTGGGTGGGTGCTCACAGGCATCCCTGTCCATGGAGGATGAGCCGAGACCTGGGGGT,10134169436,AS_RF 10-134169436-G-GGTGGGTGGGTGCTCACAGGCATCCCTGTCCATGGAGGATGAGCCGAGACCTGGGGGT,10134169436,AB_MEDIAN 11-76908662-T-TGCTCCCAGTCCCTTGCTCTGTAGCTCCAGCCCACAGCCTACAAATTCTCAGGTACCCCGCAGCCTGCAAC,11076908662,AS_RF 11-76908662-T-TGCTCCCAGTCCCTTGCTCTGTAGCTCCAGCCCACAGCCTACAAATTCTCAGGTACCCCGCAGCCTGCAAC,11076908662,AB_MEDIAN 10-135105969-T-TCCCTGTGTCCCGGGGAGCCCTACCTGTATGGGAGAGGGCAGCACGCG,10135105969,AS_RF 10-135105969-T-TCCCTGTGTCCCGGGGAGCCCTACCTGTATGGGAGAGGGCAGCACGCG,10135105969,AB_MEDIAN 9-78790221-TAGAATAGAACAGAAC-T,9078790221,AS_RF 9-78790221-TAGAATAGAACAGAAC-T,9078790221,AB_MEDIAN 9-78790226-TAGAACAGAAC-T,9078790226,AS_RF 9-78790226-TAGAACAGAAC-T,9078790226,AB_MEDIAN 9-78790230-A-AT,9078790230,AS_RF 9-78790230-A-AT,9078790230,AB_MEDIAN 9-78790246-TAGAAC-T,9078790246,AS_RF 9-78790246-TAGAAC-T,9078790246,AB_MEDIAN 20-60888872-C-CGAGGGGTGGCGAGTGGGCACGGAGAGAT,20060888872,AS_RF 20-60888872-C-CGAGGGGTGGCGAGTGGGCACGGAGAGAT,20060888872,AB_MEDIAN 9-110046005-GCCGCGTGC-G,9110046005,AS_RF 9-110046005-GCCGCGTGC-G,9110046005,AB_MEDIAN 9-110046018-C-A,9110046018,AS_RF 9-110046018-C-A,9110046018,AB_MEDIAN 18-56149291-G-GAAACATAGCTTTTAAAAACAGGACACTTTCATCAGTTTAAAAAGAAAAACTTGAAAGGGAAAACTAATGGTGCA,18056149291,AS_RF 18-56149291-G-GAAACATAGCTTTTAAAAACAGGACACTTTCATCAGTTTAAAAAGAAAAACTTGAAAGGGAAAACTAATGGTGCA,18056149291,AB_MEDIAN 18-77090093-C-CTGGAAGAGGAGGTATGTGAGTGACTCTAGCGTGGTTCACAGTGTTTCTA,18077090093,AS_RF 18-77090093-C-CTGGAAGAGGAGGTATGTGAGTGACTCTAGCGTGGTTCACAGTGTTTCTA,18077090093,AB_MEDIAN 9-136083183-T-TTAACCCTCAGCTTCCCCATCCC,9136083183,AS_RF 9-136083183-T-TTAACCCTCAGCTTCCCCATCCC,9136083183,AB_MEDIAN 9-136083195-T-TTCCCCATCCCTAACCCTCAGCC,9136083195,AS_RF 9-136083195-T-TTCCCCATCCCTAACCCTCAGCC,9136083195,AB_MEDIAN 9-139222226-CGGGCCG-C,9139222226,AS_RF 9-139222226-CGGGCCG-C,9139222226,AB_MEDIAN 9-139229149-C-CGGGTGAGTGGGGCGGCCCTGCTGGCGCGGTGAGTGGGGACGGCCCTGCTGGT,9139229149,AS_RF 9-139229149-C-CGGGTGAGTGGGGCGGCCCTGCTGGCGCGGTGAGTGGGGACGGCCCTGCTGGT,9139229149,AB_MEDIAN 9-139275864-A-AGTGGAAAGCAGCCCCAGCTCCCATGGGCACAGGGGGATGG,9139275864,AS_RF 9-139275864-A-AGTGGAAAGCAGCCCCAGCTCCCATGGGCACAGGGGGATGG,9139275864,AB_MEDIAN 9-139650819-T-TCAGGGAACAGCATGGGGAACAGTGCAGGGAACAGCACAGAGAACAGTG,9139650819,AS_RF 9-139650819-T-TCAGGGAACAGCATGGGGAACAGTGCAGGGAACAGCACAGAGAACAGTG,9139650819,AB_MEDIAN 9-139697272-G-GGGCCAGCCCTCTTGGATCTTCGGATGGGGTCAAGGTGAGCTCAGGGCCCAGGGCTGGGGGCCCCCCAA,9139697272,AS_RF 9-139697272-G-GGGCCAGCCCTCTTGGATCTTCGGATGGGGTCAAGGTGAGCTCAGGGCCCAGGGCTGGGGGCCCCCCAA,9139697272,AB_MEDIAN 19-7810559-C-CGGGTCAGCTCCTGGTAGATCTCCTGCTGCTTAGATTTCTCTGGAAGCTCACCCACTGCAGCCTTCAGCT,19007810559,AS_RF 19-7810559-C-CGGGTCAGCTCCTGGTAGATCTCCTGCTGCTTAGATTTCTCTGGAAGCTCACCCACTGCAGCCTTCAGCT,19007810559,AB_MEDIAN 17-4448002-C-CGCACAGGGAGGCGGGGGTGGGT,17004448002,AS_RF 17-4448002-C-CGCACAGGGAGGCGGGGGTGGGT,17004448002,AB_MEDIAN 19-9577391-T-TTCCTTACATTTATAGGGCTTCTCTCCAGTGTGAATTCGCACATGATTAGTAAGATCTGAATGACAAGTGAAGGCTTTCCCACAG,19009577391,AS_RF 19-9577391-T-TTCCTTACATTTATAGGGCTTCTCTCCAGTGTGAATTCGCACATGATTAGTAAGATCTGAATGACAAGTGAAGGCTTTCCCACAG,19009577391,AB_MEDIAN 19-12430053-C-CAAGGCTTTAGAACACTGCTTACATTCATACGGTTTCTCCCCAGTGTGCATTCTCTCATGTCTTCGATAGGAACTGTAAAAAGGA,19012430053,AS_RF 19-12430053-C-CAAGGCTTTAGAACACTGCTTACATTCATACGGTTTCTCCCCAGTGTGCATTCTCTCATGTCTTCGATAGGAACTGTAAAAAGGA,19012430053,AB_MEDIAN 19-14508665-A-C,19014508665,AS_RF 19-14508665-A-C,19014508665,AB_MEDIAN 19-20229941-A-ACATAAGATAATTCATACTGGAGCGAAACCCTACAAATGTGAAGAATGTGGCAAAGCCTTTAAGCGCTCCTCACAGCTTACTAGT,19020229941,AS_RF 19-20229941-A-ACATAAGATAATTCATACTGGAGCGAAACCCTACAAATGTGAAGAATGTGGCAAAGCCTTTAAGCGCTCCTCACAGCTTACTAGT,19020229941,AB_MEDIAN 19-21132852-A-AATGTGAAGAATGTGGCAAAGCTTTTAACCAATCCTCAAAACTTACCAAACATAAGAAAATTCATACTGGAGAGAAACCCTACAC,19021132852,AS_RF 19-21132852-A-AATGTGAAGAATGTGGCAAAGCTTTTAACCAATCCTCAAAACTTACCAAACATAAGAAAATTCATACTGGAGAGAAACCCTACAC,19021132852,AB_MEDIAN 17-39258135-G-GCAGCAGCTGGGGTGGCAGCAGGTGGGCTGGAAGCACACGGAATGGCAGCACTGGGGTCTGCAGCAGCTGGACACA,17039258135,AS_RF 17-39258135-G-GCAGCAGCTGGGGTGGCAGCAGGTGGGCTGGAAGCACACGGAATGGCAGCACTGGGGTCTGCAGCAGCTGGACACA,17039258135,AB_MEDIAN 17-39324229-T-TGCAGCAGCTGGGTTTGCAGCAGCTGGAGATACAGCAGGAAGGCCTGCAGCAACTGGAAATGCAGCAGCTGGGGCGGCAGCAGGTGGTCCTGCAGCAGGTGGTCTG,17039324229,AS_RF 17-39324229-T-TGCAGCAGCTGGGTTTGCAGCAGCTGGAGATACAGCAGGAAGGCCTGCAGCAACTGGAAATGCAGCAGCTGGGGCGGCAGCAGGTGGTCCTGCAGCAGGTGGTCTG,17039324229,AB_MEDIAN 19-39225008-G-GGGGTGGAGGTATGGGCCCTGGCTACAGGAAAAACAAAGTCAAACCACAGCACTTCCTGCATTCTGGCCACCACTTTAAGGGCT,19039225008,AS_RF 19-39225008-G-GGGGTGGAGGTATGGGCCCTGGCTACAGGAAAAACAAAGTCAAACCACAGCACTTCCTGCATTCTGGCCACCACTTTAAGGGCT,19039225008,AB_MEDIAN 19-42400883-T-TCCTCTCACCTCCCCC,19042400883,AS_RF 19-42400883-T-TCCTCTCACCTCCCCC,19042400883,AB_MEDIAN 19-48343262-A-ACCCTTTCTCTTCTGAATCTGCTTCCCTGCAGTTTAGATCCCGGGATGGCATTCCTGAGAAAGCAACCCGAACCAGCTGTCCTTC,19048343262,AS_RF 19-48343262-A-ACCCTTTCTCTTCTGAATCTGCTTCCCTGCAGTTTAGATCCCGGGATGGCATTCCTGAGAAAGCAACCCGAACCAGCTGTCCTTC,19048343262,AB_MEDIAN 17-61513517-T-TGGGAGGTGAGAGAGGGAACGTGAGTGCATCCGCCTGTGCGTGAGGCCTCCTGCCCCAGCAGCAAGGAGGCACCTTGGTG,17061513517,AS_RF 17-61513517-T-TGGGAGGTGAGAGAGGGAACGTGAGTGCATCCGCCTGTGCGTGAGGCCTCCTGCCCCAGCAGCAAGGAGGCACCTTGGTG,17061513517,AB_MEDIAN 19-53086440-C-CACTGGAGAGAAACCTTACAAGTGTAATGAGTGTGGCAAGACCTTTGTTCAAAATTCATCTCTTGTAATGCATAAGGTCATTCAT,19053086440,AS_RF 19-53086440-C-CACTGGAGAGAAACCTTACAAGTGTAATGAGTGTGGCAAGACCTTTGTTCAAAATTCATCTCTTGTAATGCATAAGGTCATTCAT,19053086440,AB_MEDIAN 19-54598933-A-AGCTGGAGGACTAGACTCCTGGATCTGAGGGAGGAGGG,19054598933,AS_RF 19-54598933-A-AGCTGGAGGACTAGACTCCTGGATCTGAGGGAGGAGGG,19054598933,DP_MEDIAN 17-78064020-CGGGACGCGCGCAGGCACGTGCACGAACAACACGGGACGCGCGCGGGCACGTGCACGAACAACACGGGACGCGCGCAGGCACGTGCACGAACAACACGGGACGCGCGCAGGCACGTGCACGAACAA-C,17078064020,AS_RF 17-78064020-CGGGACGCGCGCAGGCACGTGCACGAACAACACGGGACGCGCGCGGGCACGTGCACGAACAACACGGGACGCGCGCAGGCACGTGCACGAACAACACGGGACGCGCGCAGGCACGTGCACGAACAA-C,17078064020,AB_MEDIAN 17-78064169-G-GAACACAGGACACACACAGCACGTGCATGAAC,17078064169,AS_RF 17-78064169-G-GAACACAGGACACACACAGCACGTGCATGAAC,17078064169,AB_MEDIAN 19-55967240-A-AGGGTCTGAGGGAGGAGGGGCTGGGCCTGGACTCCT,19055967240,AS_RF 19-55967240-A-AGGGTCTGAGGGAGGAGGGGCTGGGCCTGGACTCCT,19055967240,AB_MEDIAN 19-56001372-G-GCGTGCCCTCCTGCCCCCCCCAGGGGAGA,19056001372,AS_RF 19-56001372-G-GCGTGCCCTCCTGCCCCCCCCAGGGGAGA,19056001372,AB_MEDIAN 19-56052853-A-T,19056052853,AS_RF 19-56052853-A-T,19056052853,DP_MEDIAN 17-78409975-A-ATTCCTGATCGAACGCGGTGGTGAGAGCACACGTCCTCGTCTCG,17078409975,AS_RF 17-78409975-A-ATTCCTGATCGAACGCGGTGGTGAGAGCACACGTCCTCGTCTCG,17078409975,AB_MEDIAN 17-79862824-A-AGGGCAGGGTAAGTCTAGCAGAGAGCGCCCATGAGGCGGCTCCGAGGGG,17079862824,AS_RF 17-79862824-A-AGGGCAGGGTAAGTCTAGCAGAGAGCGCCCATGAGGCGGCTCCGAGGGG,17079862824,AB_MEDIAN

Genomes

variant_id,xpos,metric X-6451809-T-TCTCGCTCTCCTGACTCAGTGGTTCCTCCACCTGGCTCTCCTGACTCAGTGGTTCTTCCAC,23006451809,AS_RF X-6451809-T-TCTCGCTCTCCTGACTCAGTGGTTCCTCCACCTGGCTCTCCTGACTCAGTGGTTCTTCCAC,23006451809,AB_MEDIAN X-34148805-C-CGAGACTGGACGTCCGACGAGTCTTGGGAGGCTCCGAGCG,23034148805,AS_RF X-34148805-C-CGAGACTGGACGTCCGACGAGTCTTGGGAGGCTCCGAGCG,23034148805,AB_MEDIAN X-49454149-T-TA,23049454149,AS_RF X-49454149-T-TA,23049454149,AB_MEDIAN 1-10702247-A-AGGGGGGGGGGGGGGGGGG,1010702247,AS_RF 1-10702247-A-AGGGGGGGGGGGGGGGGGG,1010702247,DP_MEDIAN X-103494998-TGGGTGGCAGAGGCGCCATGGGCGGCCCGGGTGGCAGAGGCGCCATGGGCGGCCC-T,23103494998,AS_RF X-103494998-TGGGTGGCAGAGGCGCCATGGGCGGCCCGGGTGGCAGAGGCGCCATGGGCGGCCC-T,23103494998,AB_MEDIAN X-103494998-T-TGGGTGGCAGAGGCGCCATGGGCGGCCC,23103494998,AS_RF X-103494998-T-TGGGTGGCAGAGGCGCCATGGGCGGCCC,23103494998,AB_MEDIAN 2-87141069-C-CGGCCTCGACCTGGCGGGGCGGTGGCCTCGACCTGGCGGGGCGGT,2087141069,AS_RF 2-87141069-C-CGGCCTCGACCTGGCGGGGCGGTGGCCTCGACCTGGCGGGGCGGT,2087141069,AB_MEDIAN 2-242695022-A-AGGGTTGGAGCCACACCTGGTCTGGGGCATTCGCTGTCCTGGGTCAGAGCCCCTCCTGGTCTGGGACATTCGCTGTCTG,2242695022,AS_RF 2-242695022-A-AGGGTTGGAGCCACACCTGGTCTGGGGCATTCGCTGTCCTGGGTCAGAGCCCCTCCTGGTCTGGGACATTCGCTGTCTG,2242695022,AB_MEDIAN 3-197544223-G-GCGTGTGTGTGTGTGTGTC,3197544223,AS_RF 3-197544223-G-GCGTGTGTGTGTGTGTGTC,3197544223,AB_MEDIAN 4-1388441-A-ATGCCCATGTGGAGTGCCCGCCTGCTCACACG,4001388441,AS_RF 4-1388441-A-ATGCCCATGTGGAGTGCCCGCCTGCTCACACG,4001388441,AB_MEDIAN 5-492197-A-AGGGAGGGAGGTCAGGGCCGGGCTGTGAGGGAG,5000492197,AS_RF 5-492197-A-AGGGAGGGAGGTCAGGGCCGGGCTGTGAGGGAG,5000492197,AB_MEDIAN 5-167655153-A-ATCTGTTACCACAGAGTGGGAGGGGATATACACTTTCCTCACAGAGCTGAGAAAGTTTC,5167655153,AS_RF 5-167655153-A-ATCTGTTACCACAGAGTGGGAGGGGATATACACTTTCCTCACAGAGCTGAGAAAGTTTC,5167655153,AB_MEDIAN 5-167655153-A-ATCTGTTACCACAGAGTGGGAGGGGATGTACACTTTCCTCACAGAGCTGAGAAAGTTTC,5167655153,AS_RF 5-167655153-A-ATCTGTTACCACAGAGTGGGAGGGGATGTACACTTTCCTCACAGAGCTGAGAAAGTTTC,5167655153,AB_MEDIAN 6-30997500-A-AAGGCTCTGAGACCACCACAGCCTCCACTGC,6030997500,AS_RF 6-30997500-A-AAGGCTCTGAGACCACCACAGCCTCCACTGC,6030997500,AB_MEDIAN 6-158483184-A-ACGTCAGTCCACGGTGAGGCTCGCTGCGCACTGTGCCGCGTCTTCTGCTGGGGGGAAG,6158483184,AS_RF 6-158483184-A-ACGTCAGTCCACGGTGAGGCTCGCTGCGCACTGTGCCGCGTCTTCTGCTGGGGGGAAG,6158483184,AB_MEDIAN 7-142494029-GGTCCCTAGC-G,7142494029,AS_RF 7-142494029-GGTCCCTAGC-G,7142494029,AB_MEDIAN 7-142494034-C-G,7142494034,AS_RF 7-142494034-C-G,7142494034,AB_MEDIAN 7-142494041-G-T,7142494041,AS_RF 7-142494041-G-T,7142494041,AB_MEDIAN 8-145486792-GCC-G,8145486792,AS_RF 8-145486792-GCC-G,8145486792,AB_MEDIAN 8-145537346-G-GCCC,8145537346,AS_RF 8-145537346-G-GCCC,8145537346,AB_MEDIAN 9-138150754-T-TCGGTGATGCCCACTGTATGGGGTGACGGTGGTGATGCCGACCGCATGGGGTGACGGCGGTGATGCCGACTGTATGGGGTGACGGCGGTGATGCCGACCGTATGGGGTGATGG,9138150754,AS_RF 9-138150754-T-TCGGTGATGCCCACTGTATGGGGTGACGGTGGTGATGCCGACCGCATGGGGTGACGGCGGTGATGCCGACTGTATGGGGTGACGGCGGTGATGCCGACCGTATGGGGTGATGG,9138150754,AB_MEDIAN 9-139229149-C-CGGGTGAGTGGGGCGGCCCTGCTGGCGCGGTGAGTGGGGACGGCCCTGCTGGT,9139229149,AS_RF 9-139229149-C-CGGGTGAGTGGGGCGGCCCTGCTGGCGCGGTGAGTGGGGACGGCCCTGCTGGT,9139229149,AB_MEDIAN 9-139650819-T-TCAGGGAACAGCATGGGGAACAGTGCAGGGAACAGCACAGAGAACAGTG,9139650819,AS_RF 9-139650819-T-TCAGGGAACAGCATGGGGAACAGTGCAGGGAACAGCACAGAGAACAGTG,9139650819,AB_MEDIAN 11-1902837-G-GCCTCGAGGGCGGGCGCTGGGCAGAGCAGGGCTCCCTCTGGA,11001902837,AS_RF 11-1902837-G-GCCTCGAGGGCGGGCGCTGGGCAGAGCAGGGCTCCCTCTGGA,11001902837,AB_MEDIAN 11-44096282-A-ATCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTT,11044096282,AS_RF 11-44096282-A-ATCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTT,11044096282,AB_MEDIAN 11-44096282-A-ATCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTT,11044096282,AS_RF 11-44096282-A-ATCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTT,11044096282,AB_MEDIAN 11-47422503-T-TCTGAAGGGCAGAAGGGAACTGTCCTTCAGCCAGAGCTGG,11047422503,AS_RF 11-47422503-T-TCTGAAGGGCAGAAGGGAACTGTCCTTCAGCCAGAGCTGG,11047422503,AB_MEDIAN 12-40878923-T-TTATCAGCTGGAGTGACAGGGACAACTGGATTGTCAACTGAAGTGACAGGAACAACTGGACCATCAGCTGGGGTGACAAGGACTACTGGAC,12040878923,AS_RF 12-40878923-T-TTATCAGCTGGAGTGACAGGGACAACTGGATTGTCAACTGAAGTGACAGGAACAACTGGACCATCAGCTGGGGTGACAAGGACTACTGGAC,12040878923,AB_MEDIAN 13-111109177-AACCCCAGGCGTCCGTGGGGCTGATGCCCTGCGTCTGCGTGGGACCCCAGGCGTCCGTGGGGCTGATGCCGTGCGTCTGCGTGGG-A,13111109177,AS_RF 13-111109177-AACCCCAGGCGTCCGTGGGGCTGATGCCCTGCGTCTGCGTGGGACCCCAGGCGTCCGTGGGGCTGATGCCGTGCGTCTGCGTGGG-A,13111109177,AB_MEDIAN 13-111109205-C-CTGCGTCTGCGTGGGACCCCAGGCGTCCGTGGGGCTGATGCCG,13111109205,AS_RF 13-111109205-C-CTGCGTCTGCGTGGGACCCCAGGCGTCCGTGGGGCTGATGCCG,13111109205,AB_MEDIAN 15-23686348-T-TTCTCCACCTGCTCCCACATCTTCTCCTGCTCCCGCATCCTCTCCTCCTTCTCCCGTAGCCTCTCGTCCTGCTCCCACATCC,15023686348,AS_RF 15-23686348-T-TTCTCCACCTGCTCCCACATCTTCTCCTGCTCCCGCATCCTCTCCTCCTTCTCCCGTAGCCTCTCGTCCTGCTCCCACATCC,15023686348,AB_MEDIAN 15-75129816-C-CACACGAGCCACAGCGCAGTGCCGAGCAAGTGAGAGAGTGAAGGACGGGG,15075129816,AS_RF 15-75129816-C-CACACGAGCCACAGCGCAGTGCCGAGCAAGTGAGAGAGTGAAGGACGGGG,15075129816,AB_MEDIAN 18-2614481-AG-A,18002614481,AS_RF 18-2614481-AG-A,18002614481,AB_MEDIAN 19-7938307-G-GC,19007938307,AS_RF 19-7938307-G-GA,19007938307,AS_RF 19-24309603-A-ATGTGAAGAATGTGGTGAAGCTTTTAATCGATCCTCAAATCTTACTACACATAAGATAATTCATACTGGAGAGAAACCTTACAAG,19024309603,AS_RF 19-24309603-A-ATGTGAAGAATGTGGTGAAGCTTTTAATCGATCCTCAAATCTTACTACACATAAGATAATTCATACTGGAGAGAAACCTTACAAG,19024309603,AB_MEDIAN 22-20780025-CGCGG-C,22020780025,AS_RF 22-20780025-CGCGG-C,22020780025,AB_MEDIAN 22-30772476-C-CCAGCCCTGCACATCCCCACCTCGG,22030772476,AS_RF 22-30772476-C-CCAGCCCTGCACATCCCCACCTCGG,22030772476,AB_MEDIAN

nawatts commented 6 years ago

Hi @niab,

We're no longer using this code internally, and so have no plans to fix this.