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  • running samtools mpileup with nohup -redirect STDERR?

    I have seen multiple people getting this error - when piping mpileup into bcftoos -
    [bcf_sync] incorrect number of fields (0 != 5). Corrupted file?
    I was getting this error until I saw this command does not work without redirecting STDERR -
    can someone tell me how to do this so I can run this command with nohup?

    samtools mpileup -I -C 0 -Q 40 -u -f /hg19.fasta /7623X1_Converted_reheaded.bam | bcftools view -vcg - > /7623X1.var.raw3
    thanks!

  • #2
    The bcftools view command is loads faster than the mpileup, you could run the sequentially. You won't lose much time.

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