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questions about samtools mpileup & bcftools

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  • questions about samtools mpileup & bcftools

    some silly questions:

    1. -F FLOAT minimum fraction of gapped reads for candidates [0.002]
    what's the meaning of gapped reads? does that mean the reads are juntion reads?
    for example:B810KBABXX:8:27:6656:80899#ACAGTGAT 99 chr1 509019 255 76M2010N24M = 511155 0 TCTCCTCCAAGACAACCCGCTGTCCGTCCAGACTCGATATAGGGGCTCCGAGGTCCAGGGGCTCCTTCTCTCCACTCAGCCTCACCAGCAGGCCACTGAG FFF+FGGGGGHHFHHHHHHHHFCHHHFH?HCGFDGEEEFEHDHHBFEFHB9AD<DFDEEBE:[email protected]?HFFHBBHFEHCF9:/:76 NM:i:0 XS:A:- NH:i:1

    2.are there any parameters to filter or control the mismatch near to or just in the end of a read?

    3.what's the meaning of 'cap mapping quality'?
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