1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 chromosome 1 gatk input file ../gatk/alleles/alleles.chr1.txt plat input file ../platypus/alleles/alleles.chr1.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 1368271 PLAT 1940882 Number only in PLAT 670593 Number in both 1270289 Number with ref matches 1270289 Number with ALT mismatches 23 Number of SNPs in both with all genotype matches 145109 output only GATK file written Number of SNPs only in GATK 97982 Number of error keys 0 Check number in both 1270289 chromosome 2 gatk input file ../gatk/alleles/alleles.chr2.txt plat input file ../platypus/alleles/alleles.chr2.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 1148803 PLAT 1608185 Number only in PLAT 547298 Number in both 1060887 Number with ref matches 1060887 Number with ALT mismatches 27 Number of SNPs in both with all genotype matches 112986 output only GATK file written Number of SNPs only in GATK 87916 Number of error keys 0 Check number in both 1060887 chromosome 3 gatk input file ../gatk/alleles/alleles.chr3.txt plat input file ../platypus/alleles/alleles.chr3.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 1070160 PLAT 1528194 Number only in PLAT 532469 Number in both 995725 Number with ref matches 995725 Number with ALT mismatches 27 Number of SNPs in both with all genotype matches 101433 output only GATK file written Number of SNPs only in GATK 74435 Number of error keys 0 Check number in both 995725 chromosome 4 gatk input file ../gatk/alleles/alleles.chr4.txt plat input file ../platypus/alleles/alleles.chr4.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 1015805 PLAT 1474867 Number only in PLAT 545482 Number in both 929385 Number with ref matches 929385 Number with ALT mismatches 33 Number of SNPs in both with all genotype matches 107306 output only GATK file written Number of SNPs only in GATK 86420 Number of error keys 0 Check number in both 929385 chromosome 5 gatk input file ../gatk/alleles/alleles.chr5.txt plat input file ../platypus/alleles/alleles.chr5.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 953110 PLAT 1351075 Number only in PLAT 473035 Number in both 878040 Number with ref matches 878040 Number with ALT mismatches 21 Number of SNPs in both with all genotype matches 68891 output only GATK file written Number of SNPs only in GATK 75070 Number of error keys 0 Check number in both 878040 chromosome 6 gatk input file ../gatk/alleles/alleles.chr6.txt plat input file ../platypus/alleles/alleles.chr6.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 1083513 PLAT 1571639 Number only in PLAT 593256 Number in both 978383 Number with ref matches 978383 Number with ALT mismatches 29 Number of SNPs in both with all genotype matches 113009 output only GATK file written Number of SNPs only in GATK 105130 Number of error keys 0 Check number in both 978383 chromosome 7 gatk input file ../gatk/alleles/alleles.chr7.txt plat input file ../platypus/alleles/alleles.chr7.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 925146 PLAT 1361501 Number only in PLAT 516653 Number in both 844848 Number with ref matches 844848 Number with ALT mismatches 33 Number of SNPs in both with all genotype matches 71551 output only GATK file written Number of SNPs only in GATK 80298 Number of error keys 0 Check number in both 844848 chromosome 8 gatk input file ../gatk/alleles/alleles.chr8.txt plat input file ../platypus/alleles/alleles.chr8.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 927758 PLAT 1298014 Number only in PLAT 440382 Number in both 857632 Number with ref matches 857632 Number with ALT mismatches 24 Number of SNPs in both with all genotype matches 170865 output only GATK file written Number of SNPs only in GATK 70126 Number of error keys 0 Check number in both 857632 chromosome 9 gatk input file ../gatk/alleles/alleles.chr9.txt plat input file ../platypus/alleles/alleles.chr9.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 800736 PLAT 1126138 Number only in PLAT 383429 Number in both 742709 Number with ref matches 742709 Number with ALT mismatches 11 Number of SNPs in both with all genotype matches 78054 output only GATK file written Number of SNPs only in GATK 58027 Number of error keys 0 Check number in both 742709 chromosome 10 gatk input file ../gatk/alleles/alleles.chr10.txt plat input file ../platypus/alleles/alleles.chr10.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 839715 PLAT 1198431 Number only in PLAT 417434 Number in both 780997 Number with ref matches 780997 Number with ALT mismatches 12 Number of SNPs in both with all genotype matches 73874 output only GATK file written Number of SNPs only in GATK 58718 Number of error keys 0 Check number in both 780997 chromosome 11 gatk input file ../gatk/alleles/alleles.chr11.txt plat input file ../platypus/alleles/alleles.chr11.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 761131 PLAT 1065408 Number only in PLAT 365384 Number in both 700024 Number with ref matches 700024 Number with ALT mismatches 13 Number of SNPs in both with all genotype matches 87873 output only GATK file written Number of SNPs only in GATK 61107 Number of error keys 0 Check number in both 700024 chromosome 12 gatk input file ../gatk/alleles/alleles.chr12.txt plat input file ../platypus/alleles/alleles.chr12.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 816634 PLAT 1188321 Number only in PLAT 449038 Number in both 739283 Number with ref matches 739283 Number with ALT mismatches 24 Number of SNPs in both with all genotype matches 94709 output only GATK file written Number of SNPs only in GATK 77351 Number of error keys 0 Check number in both 739283 chromosome 13 gatk input file ../gatk/alleles/alleles.chr13.txt plat input file ../platypus/alleles/alleles.chr13.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 764043 PLAT 1087268 Number only in PLAT 382321 Number in both 704947 Number with ref matches 704947 Number with ALT mismatches 16 Number of SNPs in both with all genotype matches 78190 output only GATK file written Number of SNPs only in GATK 59096 Number of error keys 0 Check number in both 704947 chromosome 14 gatk input file ../gatk/alleles/alleles.chr14.txt plat input file ../platypus/alleles/alleles.chr14.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 827814 PLAT 1175929 Number only in PLAT 412578 Number in both 763351 Number with ref matches 763351 Number with ALT mismatches 19 Number of SNPs in both with all genotype matches 139182 output only GATK file written Number of SNPs only in GATK 64463 Number of error keys 0 Check number in both 763351 chromosome 15 gatk input file ../gatk/alleles/alleles.chr15.txt plat input file ../platypus/alleles/alleles.chr15.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 651218 PLAT 919537 Number only in PLAT 312926 Number in both 606611 Number with ref matches 606611 Number with ALT mismatches 7 Number of SNPs in both with all genotype matches 52219 output only GATK file written Number of SNPs only in GATK 44607 Number of error keys 0 Check number in both 606611 chromosome 16 gatk input file ../gatk/alleles/alleles.chr16.txt plat input file ../platypus/alleles/alleles.chr16.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 602992 PLAT 867454 Number only in PLAT 306977 Number in both 560477 Number with ref matches 560477 Number with ALT mismatches 14 Number of SNPs in both with all genotype matches 57521 output only GATK file written Number of SNPs only in GATK 42515 Number of error keys 0 Check number in both 560477 chromosome 17 gatk input file ../gatk/alleles/alleles.chr17.txt plat input file ../platypus/alleles/alleles.chr17.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 746056 PLAT 1075716 Number only in PLAT 397616 Number in both 678100 Number with ref matches 678100 Number with ALT mismatches 32 Number of SNPs in both with all genotype matches 51755 output only GATK file written Number of SNPs only in GATK 67956 Number of error keys 0 Check number in both 678100 chromosome 18 gatk input file ../gatk/alleles/alleles.chr18.txt plat input file ../platypus/alleles/alleles.chr18.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 571559 PLAT 814324 Number only in PLAT 281238 Number in both 533086 Number with ref matches 533086 Number with ALT mismatches 7 Number of SNPs in both with all genotype matches 35952 output only GATK file written Number of SNPs only in GATK 38473 Number of error keys 0 Check number in both 533086 chromosome 19 gatk input file ../gatk/alleles/alleles.chr19.txt plat input file ../platypus/alleles/alleles.chr19.txt hash of gatk data created Number of SNPs hash of plat data created output only PLAT file written Number of SNPs GATK 385245 PLAT 547828 Number only in PLAT 189945 Number in both 357883 Number with ref matches 357883 Number with ALT mismatches 6 Number of SNPs in both with all genotype matches 32786 output only GATK file written Number of SNPs only in GATK 27362 Number of error keys 0 Check number in both 357883