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stschiff / msmc2

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msmc-input #25

Closed cfz1998 closed 3 years ago

cfz1998 commented 3 years ago

Hi, everyone! when i use msmc. It's give me " Haplotype index exceeds number of haplotypes in datafile".

The input file: `<chr1A_part1 190825 273 CAACAA chr1A_part1 11588243 9446 GACCACATCGGCCTCGTGACCACATCGGCCTCGT chr1A_part1 23877063 8727 GTTGTT chr1A_part1 26200727 1096 AATAAT chr1A_part1 26200730 3 ACTTACTT chr1A_part1 26200731 1 GAATGAAAGAATGAAA chr1A_part1 45844315 9853 CA chr1A_part1 45844329 14 TGACTCGCAAGGTTAGTGCTGACTCGCAAGGTTAGTGC chr1A_part1 58939483 6441 CT chr1A_part1 63511145 2397 CA chr1A_part1 91505100 11507 AC chr1A_part1 102772581 5193 AG chr1A_part1 104684808 558 TGTG chr1A_part1 140356838 14652 ATCACCAGTACCGGTTGCAGCAAAGAGCGCATCACAGATTGATCACCAGTACCGGTTGCAGCAAAGAGCGCATCACAGATTG chr1A_part1 144185802 1787 ATTTACCCGACTCCAGTAGATTTACCCGACTCCAGTAG chr1A_part1 149610591 2323 TGTGGCTGATCCGCGTGCCGCGCATGTTGCTCGGTGCGCTGGTCGGTGCCGGGTTAGCGTTGATTGGTGTGGCTGATCCGCGTGCCGCGCATGTTGCTCGGTGCGCTGGTCGGTGCCGGGTTAGCGTTGATTGG chr1A_part1 153854478 2269 AACGGAACGG chr1A_part1 175187092 8967 ATAT chr1A_part1 180379540 2174 AGCCCTGGTCTGCCTGGCCAACATGGCGCACCTGGCAGCCCTGGTCTGCCTGGCCAACATGGCGCACCTGGC chr1A_part1 184144032 2457 CGGCAGCGGCAG chr1A_part1 207555182 9823 GTTTGAACTCCAGCGGCAACACGCCCATGCCCACCAGGTTGGTGCGGTGGATGCGCTCGAAACCTTCGGCGACGATGTTTGAACTCCAGCGGCAACACGCCCATGCCCACCAGGTTGGTGCGGTGGATGCGCTCGAAACCTTCGGCGACGAT chr1A_part1 237257636 11899 CCGCCG chr1A_part1 248571467 4604 TCGGCAAATTCGGCAGAAAACCCATGAAACTCGGCAAATTCGGCAGAAAACCCATGAAAC chr1A_part1 257976293 3757 TACAAGTACAAG chr1A_part1 265011809 2947 AGAG chr1A_part1 302258882 15044 CTTTAAACTTTAAA chr1A_part1 320167446 7294 CAAGCGCAAGCG chr1A_part1 395436827 29799 AATTTTGCATAATTTTGCAT chr1A_part1 410847709 5021 TC chr1A_part1 410847719 10 CT chr1A_part1 419483584 3648 GT chr1A_part1 434961272 6337 GGCCGGCC chr1A_part1 435444002 257 AACACCGTCACAACACCGTCAC chr1A_part1 435867883 262 CAGGCTGCCGGGGTATACCGGCTCGTAGTAACCGGTGATCAGGCTGCCGGGGTATACCGGCTCGTAGTAACCGGTGAT chr1A_part1 445750247 3728 CATGATCACCAGGCTGCCGGCCTTGGCGCCGTTCATGATCACCAGGCTGCCGGCCTTGGCGCCGTT

`

What can i do to make msmc run and get right answer?

stschiff commented 3 years ago

You have vastly different number of haplotypes at each location. That's illegal. You need a fixed number of haplotypes in each location.