More posts like this
-
Which type of variant caller should I use in a WES normal cell line sample?
written by bompipi95 •
-
Extract somatic mutations and germline mutations from variant calling files?
written by ginnyli056 •
-
CNVkit calling strategies with matched-normal tumor
written by fbrundu
-
Variant Calling and Transcript expression from biological sample
written by Mask
-
Where to get somatic mutations from WGS data?!
written by dankoc •
-
raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
written by abedkurdi10 •
-
Somatic and Germline variant calling in ion torrent
written by inayat45shaikh •
-
Publicly available somatic variant calls for kidney cancer using WGS
written by tralynca •
-
Discrimination Between Germline And Somatic Mutations In Tumor Without The Availability Of The Norm…
written by Fred Fleche
-
Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
written by Istvan Albert
I dont think you can do that with any single line of code. Since the sequence is submitted in raw format, You have to download, perform alignment and process the samples manually according to the reads.
If you manage how to download SRR file (fastq), you can do the analysis without any coding by using public/ published workflows on Galaxy and an example WES workflow is here (https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html). Please read the manual or search on google how to download files from SRA/ENA. There are plenty of tutorials and automated scripts to address your query on downloading files from ENA/SRA. If you have preliminary coding experience, I would suggest to use either NF core prebuilt workflows or snakemake prebuilt workflows.
You can download files directly to Galaxy from the ENA Browser. e.g. Go to https://www.ebi.ac.uk/ena/browser/view/SRR212430?show=reads Click on "Show Column Selection" and check "fastq_galaxy" (assuming it's the generated fastq file you want) "Generated FASTQ files: Galaxy" column will now be visible in the table below. Click on a link in this column to start a download to Galaxy.