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Question: How do I process multiple pileup files at once with Varscan to get the vcf files?
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gravatar for ppurkayastha2010
8 months ago by
ppurkayastha2010 • 30
ppurkayastha2010 • 30 wrote:

I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN.

VARSCAN takes an input in pileup format.

I could get the pileup files for all 100 SRAs using NCBI SRA Tools. But not able to give the List of pileup files to Varscan, in order to generate VCF files.

Is there a way I could generate VCF files from all 100 pileup files at one go or a way to generate VCF files directly from NCBI SRA ?

any advice and suggestions will be appreciated..
sra snp varscan pileup • 400 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by ppurkayastha2010 • 30
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To make calls for multiple samples, Varscan expects merged pileup output from Samtools Mpileup with read groups assigned. This is different from what is extracted from NCBI (individual samples). Instead, download the fastq data from NCBI, map with BWA, run Mpileup, then Varscan. Dataset collections can be used to process the data in batch mode.

Galaxy example tutorials that cover how to use collections and perform variant analysis: https://galaxyproject.org/learn/

Most Varscan command line functions/parameters are incorporated into the Galaxy wrapper. The same is true for the upstream tools also wrapped for Galaxy. This means that if a particular use-case is not covered by a tutorial, the original tool's manuals can be useful references. Varscan user manual: http://varscan.sourceforge.net/using-varscan.html#pileup-howto

Thanks! Jen, Galaxy team
ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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