SRA to Vcf files
2
0
Entering edit mode
@naaz27khan-13819
Last seen 6.6 years ago

Hi All,

I am new in this field...Can anyone tell me how to convert the SRA file to Vcf files in R studio? Workflow or tutorial will help. Thanks

 

 

 

 

 

R • 1.3k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 15 hours ago
United States

SRA files are, in general, simply raw data (e.g., read counts with per-base quality scores). In which case you would need to convert to FASTQ, align to a genome, and then infer variants. There are any number of ways to do that, most of which don't involve any Bioconductor packages. But perhaps you mean something different? If so, can you clarify?

ADD COMMENT
0
Entering edit mode
@naaz27khan-13819
Last seen 6.6 years ago

I want to convert Fastq files into VCF files using GATK f and then visualizing variants in IGV. What are the commands to align the FASTq files to hg19 reference genome with STAR in R studio? After mapping, how files are converted to Variant file with GATK?

 

 

 

 

 

ADD COMMENT
0
Entering edit mode

If you want to make a comment, please use the ADD COMMENT button rather than adding another answer.

In addition, you want to use STAR to align, GATK to call variants, and IGV to visualize, none of which is a Bioconductor package. R Studio is an IDE for R, not any of those programs. So it appears that you are asking your question in the wrong place. You would probably get better results by simply Googling something like 'DNA-Seq workflow tutorial'.

ADD REPLY

Login before adding your answer.

Traffic: 706 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6