Mercurial > repos > devteam > vcftools_consensus
changeset 0:79f5d34da277 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit 5d67d705695dfee875bda85aa02ddf38924790a7
| author | devteam |
|---|---|
| date | Fri, 25 Nov 2016 07:30:19 -0500 |
| parents | |
| children | |
| files | test-data/output1.fasta test-data/reference.fasta test-data/sample1.vcf tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample vcftools_consensus.xml |
| diffstat | 6 files changed, 547 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.fasta Fri Nov 25 07:30:19 2016 -0500 @@ -0,0 +1,168 @@ +>Chromosome +TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT +AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG +ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT +GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC +CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC +GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT +ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG +GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC +GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC +GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT +TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG +GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG +GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC +AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG +GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC +GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC +CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC +ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC +ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC +GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC +GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC +GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG +GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC +AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC +CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC +ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC +TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC +CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG +ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC +TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT +TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATAACACCCGCATAA +CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC +TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCGTTC +GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT +GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT +TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC +CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT +CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG +GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC +CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT +CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG +GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC +GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG +TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT +CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG +CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG +ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG +AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG +TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG +TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC +GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC +CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA +CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG +GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC +CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG +CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT +TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG +ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT +GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC +GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT +GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG +GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC +GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGGACGGCGTTATTGAAGTCC +GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGAC +AGTCGTTTGGCGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAG +TTGGCACCGGAAGTGAAGAAGGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCT +ATCGGTTATCGGGCCAGCATGGATGTAACCGGTCCCAGCGAGCAGTCAGATACCGATCGG +CAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCCGTCGGGATGCCGAACTCGAG +CGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACTAGGCGATCAA +CCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG +GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTG +TTCGCCGAACTGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAA +CAGGTGTTGGTGACTGCCGCGGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGG +GTGCACATCGATGTGCGTGCCGATGACACCGGATCGATGTCGGTGGTTCTGCCATGACGG +GTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATCAATGAAGTCACCAGGGTTGG +ATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGCGGACAAGACG +CCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT +GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGC +TGGCAAAGAAACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGT +CTGCGGTGGTCGGCCACCAGATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGG +TGTTGAGCGTGATTGCGGAGTCGACGGCGTGGGCGACGCAGTTGAGGATCATGCAGGCCC +AGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGTGGTGCGATCGCTAAAGATCA +CCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGTAGGGGTCCGC +GCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA +GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGAT +GTCCGACGCACGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCC +CGATCACGGTACAGTGGTGTGCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCC +TGAGGAGAGTATTCGGATCGTGGCTGCCCAGAAAAAGAAGGCCCAAGACGAATACGGCGC +TGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGCAAACGTCCCGGCATGTACAT +TGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCGACAACGCGGT +CGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG +TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACC +GACCGTCGACGTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTA +TGCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCG +GCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGA +ACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTG +GGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCGCCCGCCGGCT +GCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC +CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAG +TGAACGCGCAGCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCC +GGGTGGCCTGGTGGACTTCGTGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAG +CATCGTGGACTTTTCCGGCAAGGGCACCGGGCACGAGGTGGAGATCGCGATGCAATGGAA +CGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG +CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA +CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT +GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA +GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA +CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC +GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA +CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA +ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT +GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA +CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA +CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA +TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC +GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA +GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG +GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG +TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG +TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA +GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA +TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC +CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCCAGCAGGAGATGCAGCGCA +GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG +GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG +ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC +ACGGCGACGCGTCGATCTACGACACCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT +ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA +TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG +AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC +CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA +CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA +ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG +ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG +GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA +CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA +TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA +GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG +TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG +CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG +ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC +GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC +TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA +TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG +AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG +ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG +TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG +ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA +AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG +CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA +TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG +CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC +GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA +CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG +GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG +CCGACGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG +ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA +TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA +CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG +GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA +TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG +CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG +GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG +CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG +CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT +GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC +GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Fri Nov 25 07:30:19 2016 -0500 @@ -0,0 +1,168 @@ +>Chromosome +TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT +AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG +ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT +GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC +CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC +GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT +ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG +GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC +GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC +GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT +TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG +GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG +GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC +AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG +GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC +GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC +CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC +ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC +ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC +GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC +GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC +GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG +GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC +AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC +CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC +ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC +TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC +CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG +ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC +TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT +TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAA +CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC +TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCATTC +GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT +GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT +TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC +CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT +CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG +GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC +CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT +CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG +GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC +GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG +TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT +CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG +CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG +ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG +AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG +TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG +TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC +GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC +CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA +CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG +GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC +CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG +CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT +TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG +ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT +GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC +GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT +GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG +GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC +GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGGACGGCGTTATTGAAGTCC +GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGAC +AGTCGTTTGGCGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAG +TTGGCACCGGAAGTGAAGAAGGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCT +ATCGGTTATCGGGCCAGCATGGATGTAACCGGTCCCAGCGAGCAGTCAGATATCGATCGG +CAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCCGTCGGGATGCCGAACTCGAG +CGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACTAGGCGATCAA +CCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG +GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTG +TTCGCCGAACTGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAA +CAGGTGTTGGTGACTGCCGCGGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGG +GTGCACATCGATGTGCGTGCCGATGACACCGGATCGATGTCGGTGGTTCTGCCATGACGG +GTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATCAATGAAGTCACCAGGGTTGG +ATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGCGGACAAGACG +CCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT +GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGC +TGGCAAAGAAACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGT +CTGCGGTGGTCGGCCACCAGATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGG +TGTTGAGCGTGATTGCGGAGTCGACGGCGTGGGCGACGCAGTTGAGGATCATGCAGGCCC +AGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGTGGTGCGATCGCTAAAGATCA +CCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGTAGGGGTCCGC +GCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA +GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGAT +GTCCGACGCACGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCC +CGATCACGGTACAGTGGTGTGCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCC +TGAGGAGAGTATTCGGATCGTGGCTGCCCAGAAAAAGAAGGCCCAAGACGAATACGGCGC +TGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGCAAACGTCCCGGCATGTACAT +TGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCGACAACGCGGT +CGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG +TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACC +GACCGTCGACGTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTA +TGCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCG +GCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGA +ACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTG +GGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCGCCCGCCGGCT +GCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC +CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAG +TGAACGCGCAGCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCC +GGGTGGCCTGGTGGACTTCGTGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAG +CATCGTGGACTTTTCCGGCAAGGGCACCGGGCACGAGGTGGAGATCGCGATGCAATGGAA +CGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG +CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA +CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT +GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA +GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA +CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC +GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA +CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA +ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT +GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA +CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA +CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA +TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC +GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA +GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG +GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG +TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG +TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA +GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA +TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC +CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCGAGCAGGAGATGCAGCGCA +GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG +GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG +ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC +ACGGCGACGCGTCGATCTACGACAGCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT +ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA +TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG +AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC +CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA +CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA +ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG +ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG +GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA +CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA +TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA +GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG +TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG +CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG +ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC +GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC +TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA +TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG +AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG +ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG +TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG +ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA +AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG +CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA +TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG +CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC +GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA +CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG +GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG +CCGGCGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG +ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA +TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA +CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG +GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA +TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG +CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG +GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG +CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG +CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT +GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC +GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1.vcf Fri Nov 25 07:30:19 2016 -0500 @@ -0,0 +1,98 @@ +##fileformat=VCFv4.1 +##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> +##FILTER=<ID=LowQual,Description="Low quality"> +##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:35:17 SAST 2015",Epoch=1433669717749,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2997_878#L6-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> +##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) +##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive) +##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive) +##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive) +##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive) +##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive) +##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive) +##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive) +##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive) +##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive) +##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive) +##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive) +##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive) +##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive) +##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive) +##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive) +##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive) +##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive) +##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive) +##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive) +##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive) +##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive) +##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive) +##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive) +##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive) +##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive) +##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive) +##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive) +##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive) +##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive) +##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive) +##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive) +##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive) +##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive) +##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive) +##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive) +##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive) +##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive) +##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive) +##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive) +##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive) +##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive) +##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive) +##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive) +##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive) +##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive) +##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive) +##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive) +##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive) +##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive) +##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive) +##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive) +##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive) +##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive) +##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive) +##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive) +##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive) +##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive) +##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive) +##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive) +##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive) +##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive) +##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive) +##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive) +##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive) +##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> +##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> +##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> +##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> +##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> +##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> +##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> +##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> +##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> +##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> +##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> +##contig=<ID=Chromosome,length=10000> +##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ./R_2997_878#L6-_.R +Chromosome 1849 . C A,<NON_REF> 4546 . DP=129;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,129,0:129:99:4576,0,4576:0,0,56,73 +Chromosome 1977 . A G,<NON_REF> 1957 . DP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,54,0:54:99:1987,0,1987:0,0,13,41 +Chromosome 4013 . T C,<NON_REF> 2397 . DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,66,0:66:99:2427,0,2427:0,0,31,35 +Chromosome 7362 . G C,<NON_REF> 2519 . DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,68,0:68:99:2549,0,2549:0,0,28,40 +Chromosome 7585 . G C,<NON_REF> 1295 . DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,36,0:36:99:1325,0,1325:0,0,26,10 +Chromosome 9304 . G A,<NON_REF> 1945 . DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,58,0:58:99:1975,0,1975:0,0,23,35
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Nov 25 07:30:19 2016 -0500 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 25 07:30:19 2016 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_consensus.xml Fri Nov 25 07:30:19 2016 -0500 @@ -0,0 +1,78 @@ +<tool id="vcftools_consensus" name="Consensus" version="0.1.11"> + <description>Apply VCF variants to a fasta file to create consensus sequence</description> + + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.3.2">htslib</requirement> + <requirement type="package" version="0.1.11">vcftools</requirement> + </requirements> + + <stdio> + <!--<regex match=".*" source="both" level="log" description="tool progress"/>--> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command> + <![CDATA[ + ln -s '${variants}' variants.vcf && + vcf-sort variants.vcf | bgzip -c > variants.sorted.vcf.gz && + + tabix -p vcf variants.sorted.vcf.gz && + + #if $ref_genome_source.index_source == 'history': + ln -s '${ref_genome_source.ref_file}' reference.fasta && + samtools faidx reference.fasta && + #end if + + cat + #if $ref_genome_source.index_source == 'builtin' + '${ ref_genome_source.reference_genome.fields.path }' + #else + reference.fasta + #end if + | vcf-consensus variants.sorted.vcf.gz > '${output}' + ]]> + </command> + <inputs> + <conditional name="ref_genome_source"> + <param name="index_source" type="select" label="Reference genome source"> + <option value="builtin">Built-in genome</option> + <option value="history">History</option> + </param> + <when value="builtin"> + <param name="reference_genome" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="2" type="sort_by" /> + <validator message="No suitable reference genomes found" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Reference genome" /> + </when> + </conditional> + <param name="variants" label="Datasets containing Variants" type="data" format="vcf" /> + </inputs> + + <outputs> + <data name="output" format="fasta"/> + </outputs> + + <tests> + <test> + <param name="index_source" value="history" /> + <param ftype="fasta" name="ref_file" value="reference.fasta" /> + <param ftype="vcf" name="variants" value="sample1.vcf" /> + <output name="output" ftype="fasta" file="output1.fasta" /> + </test> + </tests> + + <help> + Please see the VCFtools `documentation`__ for help and further information. + + .. __: http://vcftools.sourceforge.net/docs.html + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr330</citation> + </citations> +</tool>