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  • Varscan header doesn't match the number of columns in the data

    I'm using Varscan 2.3.3 with the somatic sub program and noticed the column names (there are 19 based on the output file) but there are 23 columns worth of data below the header. I looked at the documentation and it also shows 19 columns. Can anyone shed some light on what the 4 additional columns at the end of the file are:

    $ head -2 1.snp
    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 10469 C G 43 2 4.44% C 36 11 23.4% S Somatic 1.0 0.008838714792838208 20 16 3 8 32 11 0 2

    $ awk -F '\t' '{print NF}' 1.snp | less
    19
    23
    23
    23
    23
    23

  • #2
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    I think this thread concerns the same question
    //A

    Comment


    • #3
      Thanks, didnt catch the thread during my search. Much appreciated!

      Comment


      • #4
        Thanks for the question, rdeboja, and to adrianl for the answer. I will make sure the output is properly headered in the next release of VarScan!

        Comment

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