REF allele or missing

[baozg]

Hi, @lh3

I am using minipileup to compare three aligner for SVs calling from assmbly. But I found some inconsisance about genotype of REF allele or missing allele. So minipileup will do the strigent intersection of alleles in the population, but why this loci's genotype will be different? Did I misunderstand any setting?

Here is the command I use:

~/software/minipileup/minipileup -vcC -f Col-CC.fa -a0 -s0 -q0 -l 20000 Ler-0.aw.sorted.bam Ler-0.mm2.sorted.bam Ler-0.wfmash.sorted.bam

# anchorwave, minimap2, wfmash

Chr1    274235  .       CGATTTATTAAACACAAACAAAAAAAAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA     C       1       .       .       GT:ADF:ADR      0/0:1,0:0,0     1/1:0,1:0,0     0/0:1,0:0,0
Chr1    614499  .       T       TTTTTTTTTAGTAAGATTTGCTTACATTGACTCAACTCTTAACATAAATAACTTAAATGACACACGTTTGGTTTCAAAAACTGTAGTAACCCATATCTTTGGTAAAAAGACGAAATAACCTTAATGATTAATTGTAATCAAATTAAAACAAAAAATAAAAAATAAAACAAATCTTTTATATTTTAAAGCACAAGTCACTCCACCAATAAAATTTTGACAAATCAGCAAAACCAAATTATTTTTCAACAGAATTATAAAATCAAAAAAGAAATCGTGGATAAAAAAGAAAACCAAAACCTATATTACATAATTAAAACAAAAACGAAAATCCAGTTAACGTGAGAATAAACTTTTTAAAAAATAATAATTTTGAACAAAATTTAGATAAAGAAGAATCTTCTTCACATATTTCGTTTTTGATTTTAAAAATACTAAAGAAAAACAATTTAATTTTGATATTGCATATTATAAATTGACTTGTTTTAGCTTACCAATAATATTTTGACATGTATCAATTCACAAATAATTGATTTGATGGTAGGAATAGAAGAAGAAAAAAAACGGTTATGAAAACCCTTGGAGAATTTATCATGACTAATAAAATTCATTAAAATTCAAATATGACAATATTATGTAAAAATCTGCCGACATTAATAAAAGTCTGTCGTGACGTTATGAAAATTTCTTTTTCAAAAAAAAAAAAAAATCCAGAATCAGACCGGAAATAATTTAATTGAGGGCTAGCTAATAAATCTCATATAACAAAAAATTTCGAAATTTTAAAAATAAATCTGCTAAAAAAAGTCTGTTATTACTAAAAAGGTTATTCTAGACATAAACAAATCGGCCATAACATTGACATGAGTAAATCTGTTATGCTTTGACACTGAAAAACAAAACTGTCATCACTAAAAACAAATCTGTTATCACTATGTGACTGTGTAGTAATTTTATTTTTTAATAAAAATCTGTTGTAAAACACCAGATTTGTTAACAAGTTAATTAAATCTGTGATTACACAAAACAACTCTGTCATGCCTATATAACATTTTTCGAGGTTAACAAATCTGTTATAACACAACAGATTTTTGGGTGCAAATAGAAAATCTGTTGCCACCATAAAGAAAAATATGTGGTCCGGAAAACAAATCAGTGACAGATTTGGTTTCAACATTCTTACTTTTGAAATTTAAATAAAATCTGTGGAGACTATATGAAACAAATCAGTCACGGTTAAAAAATCTGCGAAAAAAAAAAAATCTGGCGTAACATAACACAGTAAAGTCTGTGGTACAAAACAAGTCTGTTGTAAAAAATCTGTGGTTGACCAACAAATCTGTGATCGATAACAAATCCGTCGCAACAAGAGCCACAGATTTACCAAAAACGACGATGGCATTTTCGTAAATAAATGTGGTTTTATTGCCTTGCTGGAATTAAATAGTAATGGCATTTCTGTAATACTGTTTTTCTCTGCAAAGGAAAACAAGGATAATTTAGGTATAATTATTACTCAAATAACTCATATTTTTAATTAGCATTCCTTTTGGGTCATTATGTATAAAATATGGGTTACTCTAATAAATTTCCG 1       .       .       GT:ADF:ADR      0/0:1,0:0,0     1/1:0,1:0,0     0/0:1,0:0,0

[lh3]

In both cases, minimap2_asm20 gives different alignment positions.