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  • jfeketet
    started a topic bcftools question

    bcftools question

    Hello,
    I am trying to repeat an ngs analysis made by impact pipeline (http://tanlab.ucdenver.edu/IMPACT/) and I have a problem with bcftools:
    My command is:
    samtools mpileup -C 0 -A -B -d 10000 -v -u -f hg19_exome.fa
    Tumor_deduped.bam | bcftools call -O v -v -c -n 0.05 -p 1 -
    A -o Tumor.vcf

    And I get the following error:
    bcftools: ccall.c237: update_bcf1: Assertion 'call->unseen==nals-1' failed.


    If you have any idea about this problem please let me know.

    Thank you very much in advance!
    fjeketet

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