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construct whole genome reference for HG19

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  • construct whole genome reference for HG19

    I download HG19 from ucsc, after unzip it is many files seperated by chr.

    I did
    cat chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr20.fa chr21.fa chr22.fa chrX.fa chrY.f
    a chrM.fa >hg19.fa

    to create the hg19.fa

    then I used bwa to build the index,
    ./bwa index hg19.fa
    This step has no error either.

    Then I run bwa like this

    ./bwa aln -q 15 hg19.fa sample.txt>sample.sai

    I get this error

    [bwa_aln] 17bp reads: max_diff = 2
    [bwa_aln] 38bp reads: max_diff = 3
    [bwa_aln] 64bp reads: max_diff = 4
    [bwa_aln] 93bp reads: max_diff = 5
    [bwa_aln] 124bp reads: max_diff = 6
    [bwa_aln] 157bp reads: max_diff = 7
    [bwa_aln] 190bp reads: max_diff = 8
    [bwa_aln] 225bp reads: max_diff = 9
    [bwa_read_seq] 0.0% bases are trimmed.
    [bwa_aln_core] calculate SA coordinate... Segmentation fault


    Does anyone know what could have caused this error?

  • #2
    Originally posted by foxyg View Post
    I download HG19 from ucsc, after unzip it is many files seperated by chr.
    […]

    Does anyone know what could have caused this error?
    If you run
    Code:
    $ bwa index
    you'll see this note:

    Code:
    Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
             `-a div' do not work not for long genomes. Please choose `-a'
             according to the length of the genome.
    hence you can fix it indexing like this:

    Code:
    $ bwa index -a bwtsw hg19.fa
    d

    Comment


    • #3
      Thanks I am trying this. But I have built index for single chr before without using -a option and it worked out fine.

      Comment


      • #4
        Originally posted by foxyg View Post
        Thanks I am trying this. But I have built index for single chr before without using -a option and it worked out fine.
        A single chrom is probably small enough for default "is" algorithm

        Comment

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