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  • How to use SAMtools?

    Hi all
    I am a newbie for SAMtools, trying to find SNPs. However, SAMtools (version 0.1.18)didn't return the right result.

    My command: samtools pileup -f hs_ref_GRCh37.p5_chrX.fa sub1.bam chrX > hs.txt. The result contains the information of all bases, such as:
    chrX 2 N 1 ^!t I
    chrX 3 N 1 a I
    chrX 4 N 1 a I
    chrX 5 N 1 c I
    chrX 6 N 2 c^!c II
    chrX 7 N 2 cc II
    chrX 8 N 2 tt II
    ......

    When I try 'mpileup' command, system warns:[main] unrecognized command 'mpileup'.

    Please, I need your help.
    Thanks

  • #2
    Pretty sure pileup is gone so shouldn't work. Here are commands that work for me. Not sure if this is ideal, though.

    /samtools-0.1.18/samtools mpileup -ugf [Reference_Sequence] [Aligned_File] | /samtools-0.1.18/bcftools/bcftools view -bvcg -> [Intermediate_File] &

    /samtools-0.1.18/bcftools/bcftools view [Intermediate_File] | /samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > [Called_Variants] &

    Comment


    • #3
      I got it.
      Thanks Heisman

      Comment

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