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  • swapnil2188
    Member
    • Feb 2012
    • 12
    #1

    Can VarScan be used to find out Somatic Mutations in RNA seq Data ?

    Hello,
    I am trying to find out Somatic mutations Using VarScan in RNA seq Data.
    Can Varscan detect them in RNA seq ?

    1. Has anyone used it previously on RNA ?

    2. I used the following steps:

    - samtools sort .bam

    - samtools mpileup -B -q 1 -f ref.fa tumor.sorted.bam > tumor.sorted.pileup

    - java -jar varscan somatic control.sorted.pileup tumor.sorted.pileup --output-snp somatic_output.snp --output-indel somatic_output.indel

    The commands are still running.

    I looked at the .snp and .indel files.

    The output files look this way

    chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus
    chr1 20121 N A 0 8 100% A 0 8 100% A Germline 1.6636709775210046E-9 1.0 0 0 0 8
    chr1 20122 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20123 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20124 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20125 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20126 N C 0 9 100% C 0 8 100% C Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20127 N C 0 8 100% C 0 8 100% C Germline 1.6636709775210046E-9 1.0 0 0 0 8
    chr1 20128 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20129 N C/NC 0 7 100% C 0 5 100% NC Unknown 1.0 1.0 0 0 0 5
    chr1 20130 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20131 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
    chr1 20132 N T 0 9 100% T 0 8 100% T Germline 4.2852131239177147E-10 1.0 0 0 0 8



    There are some places which show unknown and I dont find Somatic in anywhere.

    Whats the reason ?
    Are any of the above steps wrong ?

    Can anyone help me with this ?


    Thanks !
    Tags: None
    • bioliyezhang
      Member
      • Mar 2011
      • 19
      #2
      Originally posted by swapnil2188 View Post
      Hello,
      I am trying to find out Somatic mutations Using VarScan in RNA seq Data.
      Can Varscan detect them in RNA seq ?

      1. Has anyone used it previously on RNA ?

      2. I used the following steps:

      - samtools sort .bam

      - samtools mpileup -B -q 1 -f ref.fa tumor.sorted.bam > tumor.sorted.pileup

      - java -jar varscan somatic control.sorted.pileup tumor.sorted.pileup --output-snp somatic_output.snp --output-indel somatic_output.indel

      The commands are still running.

      I looked at the .snp and .indel files.

      The output files look this way

      chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus
      chr1 20121 N A 0 8 100% A 0 8 100% A Germline 1.6636709775210046E-9 1.0 0 0 0 8
      chr1 20122 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20123 N A 0 9 100% A 0 8 100% A Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20124 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20125 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20126 N C 0 9 100% C 0 8 100% C Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20127 N C 0 8 100% C 0 8 100% C Germline 1.6636709775210046E-9 1.0 0 0 0 8
      chr1 20128 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20129 N C/NC 0 7 100% C 0 5 100% NC Unknown 1.0 1.0 0 0 0 5
      chr1 20130 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20131 N G 0 9 100% G 0 8 100% G Germline 4.2852131239177147E-10 1.0 0 0 0 8
      chr1 20132 N T 0 9 100% T 0 8 100% T Germline 4.2852131239177147E-10 1.0 0 0 0 8



      There are some places which show unknown and I dont find Somatic in anywhere.

      Whats the reason ?
      Are any of the above steps wrong ?

      Can anyone help me with this ?


      Thanks !
      Hi,
      I am also very interested in this question.
      I just wonder did you solve the problem, or do you have recommended tools/pipeline to call mutations using RNAseq data?
      Thanks.

        Comment

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