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lh3 / minipileup

Simple pileup-based variant caller
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REF allele or missing #14

Closed baozg closed 2 months ago

baozg commented 2 months ago

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
image image 
# 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 commented 2 months ago

In both cases, minimap2_asm20 gives different alignment positions.