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  • bair
    replied
    Originally posted by lh3 View Post
    I thought this should never happen, but it happened... This says that at a position there are more than 64 types of indels. For now, you may use "-I" to disable indel calling.
    Thank you heng,

    But I still get outputs, there are SNPs and INDELs in vcf file, can I trust them? Does samtools ignores the problem INDELs and complete the job, or stop running?

    Leave a comment:


  • lh3
    replied
    I thought this should never happen, but it happened... This says that at a position there are more than 64 types of indels. For now, you may use "-I" to disable indel calling.

    Leave a comment:


  • bair
    started a topic samtools mpileup fails

    samtools mpileup fails

    Hello all,

    I'm using asmtools mpileup for snp calling from eight bam files, I get this following error message

    bam2bcf_indel.c:181: bcf_call_gap_prep: Assertion `n_types < 64' failed.
    [bcf_sync] incorrect number of fields (7 != 5). Corrupted file?
    [afs] 0:16195.241 1:1.758 2:87.006 3:1.843 4:16.294 5:0.378 6:3.137 7:0.193 8:4.107 9:0.037 10:0.005 11:0.000 12:3.000
    13:0.000 14:2.008 15:0.118 16:10.874

    Any helps?

    Thanks

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