Question: Visualizing mpileup data
gravatar for rquigl01
2.4 years ago by
rquigl0110 wrote:

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!

snp galaxy samtools bam • 1.2k views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson25k • written 2.4 years ago by rquigl0110
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 is a good place to start.

For help/tutorials, try:

Best, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson25k
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