So far in my analysis of my NGS data, I have ran my files through bowtie2 which created a SAM file. I then converted that SAM file into a BAM file. My ultimate goal is to have all of the SNPs, SNVs, and INDELS in a table like manner for me to look at. I'm not really sure how to achieve this after creating the BAM file. I've tried mpileup, but when I open the vcf file in IGV and start to zoom in on a chromosome position, the program freezes. I also see no way of converting that SNP data into a easy to read data format. On galaxy it says that my mpileup data has over 100 million lines. I really only want to see the SNPs and INDELS. As you can probably tell, I'm a beginner to all of this. Any help would be greatly appreciated!
There are many other tools to do Variant analysis in Galaxy. Each processes the data differently and has other output options (including tabular summaries). The tool group NGS: Variant Analysis at http://usegalaxy.org is a good place to start.
For help/tutorials, try:
- https://usegalaxy.org/page/list_published Seach by the keyword "variant"
- https://wiki.galaxyproject.org/Support - Other resources listed at top of the wiki
Best, Jen, Galaxy team