NGS pipelines @ free of cost

Question

[bharathramh]

Is there any pipeline which convert sra file to vcf @ free of cost?

Thanks in advance

Answer 1

[Sandeep]

First of all, there are plenty of files available as sra. You would need heavy computing to setup any kind of pipeline for analysis of variants. If you meet the criteria of computing power, then most of the tools available are open source, hence free for academic purpose.

Answer 2

[EagleEye]

A: FASTQs to the VCF

Use fastq-dump to convert from SRA to FASTQ.

[bharathramh]

I got the error msg when is use that

---

uday@uday:~/Desktop/NGS_files/sratoolkit.2.5.7-ubuntu64$ fastq-dump ERR445520
2016-01-02T08:30:52 fastq-dump.2.5.7 err: item not found while constructing within virtual database module - the path 'ERR445520' cannot be opened as database or table

[Ido Tamir]

You have a long way before you, and you should learn to read the manuals of the programs you are using. Its at least an --accession needed. And I don't know if ERR accessions are possible.