Interval Format Variant Files Convertion Problems And Igv And Annotation Application

Question

[Tonyzeng]

I produced .sam formal variants files by Mpileup and then converted them into .bam. however, after several steps for filtering variants, I got interval format variant files. Then I want use them with IGV and annonation software. But the default format these softwares accept is BAM, VCF or BED.... , now Is there any tools to convert these interval format files to other format files?

Here they are

chr1 3532097 3532098 T 37 0 1 0 25 26 1 3.84615384615

chr1 3532131 3532132 T 47 0 0 3 26 29 3 10.3448275862

chr1 3532174 3532175 A 21 17 0 3 0 20 3 15.0

Above are parts of interval format variant files I made by using filter pipeup tool from SAM tools. Here is the demonstrations for the above 12 columns

  1 Chromosome

  2 Position start 

  3 position end

  4 Reference base at that position

  5 Coverage (# reads aligning over that position)

  6 Number of A variants

  7 Number of C variants

  8 Number of G variants

  9 Number of T variants

 10 Quality adjusted coverage:

 11 Total number of deviants (if Convert coordinates to intervals? is set to yes)

 12 (C11/C10)x100%

[Devon Ryan]

Could you give a couple lines of one of these "interval format variant" files and mention what you used to create it? Normally filtering a VCF will end up producing a VCF still.

[Tonyzeng]

I have edited my question as above, thank yo

Answer 1

[Devon Ryan]

Assuming that this is output from the Galaxy "Filter Pileup" tool, that seems to be Galaxy-specific and actually takes a pileup as input, rather than a VCF file (in the source code for that function, it seems that the output is in a pseudo-BED format). There's no perfect way to go from this format back to the original pileup format (the quality scores are averaged here, so you can't reliably go back to the original base-call scores), so you might just skip this tool and go from pileup to vcf. There are a number of tools meant to filter at the VCF level and they'll actually produce proper VCF files as output.

[Tonyzeng]

Thank you, dpryan, I think you made the point. Since I am the new for variant filtering, are there some reliable tools to fitler at the VCF format files?