Question: Varscan2 warning : resetting normal
0
gravatar for bharata1803
3.8 years ago by
bharata1803420
Japan
bharata1803420 wrote:

Hello,

So, I have 8 normal sample and 8 tumor sample. Each normal and tumor group had been processed to get mpileup file by samtools. After that, I did the varscan2 soomatic function to call variation. After that, I got warning resetting normal and from what I found in the document, it's better to not call mpileup for each group. Instead, calling mpileup for 2 bam file, 1 normal and 1 tumor. So, I had finished doing this. I take 1 normal sample and 1 tumor sample for mpileup input to generate 1 mpileup file. After that, I use that mpileup file for varscan input. The result is no warning and seems no problem. My question is, how do I integrate the result for 8 normal/tumor pair varscan results? I figure if I proocess the data with 1 normal and 1 tumor, I will need to do varscan call 8 times and will get 8 results. Is there any method to join the results?

varscan2 alignment • 1.4k views
ADD COMMENTlink modified 3.8 years ago by russhh4.3k • written 3.8 years ago by bharata1803420
0
gravatar for russhh
3.8 years ago by
russhh4.3k
UK, U. Glasgow
russhh4.3k wrote:

I always make a combined vcf for all patients studied.

After you have your patient-specific vcfs, Merge the positions present in those files to generate a single bed.

Then, for each patient, extract the variants (and non-variants) lying in the positions in that bed using varscan somatic --validation.

The varscan-validation vcfs can then be merged.

If you'v a good number of samples, you can use the merged vcf to find biases etc

HTH

ADD COMMENTlink written 3.8 years ago by russhh4.3k

Thank you for your reply.

So, basically, you generate VCF file for each sample, not normal-tumor pair? Is the workflow like this:

1. Generate mplieup for each sample

2. Generate vcf for each mpileup

3. Merge vcf into bed

4. Use varscan validation to the bed

5. Merge the result

ADD REPLYlink written 3.8 years ago by bharata1803420

For each PATIENT I run varscan to generate a vcf; each run of varscan requires two samples: the tumour and the normal

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by russhh4.3k
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