How to read Varscan VCF output in column "Cons"?

Question

[weixiaokuan]

Hi,

I am trying to use Varscan2 to make indel calls from pileup files created by samtools. The process ran very smooth but I got confused with the output. I don't know how to read the result of the indel. For example (below is part of the VCF output):

Chrom   Position    Ref Cons
chr1    160623          C   */-TGGTCT
chr1    160634          T   */-AG
chr1    160645          A   */+TTG
chr1    160656          A   */-C
chr1    160667          T   */-CAGC
chr1    160678          A   */-GC

how to read the column, "Cons"? I have tried to find related information but no success. there is no document or example to explain this format.

Thank you!

Xiaokuan

[barslmn]

I haven't used Varscan, but this is not a valid VCF.

[weixiaokuan]

not all the VCF files will be exactly the same format. This was generated to compute indel and using "Cons" column not "ALT" Column.

[barslmn]

There can be variability between the files as much as the format specification allows. However, there is no column named “Cons” in the specification. You can try reading the files with bcftools view to see if it's a valid VCF file.