SNP but not seen in IGV

[cpwater]

Hi there:
I called SNPs using freebayes and got 2 SNPs (15725855 and 15726131) but the variant is now shown in IGV, is my process wrong or sth else?
This occurred to other sample with depth more than 5 in vcf file but nearly no in IGV.

Thanks!

[hushuzuiniu]

Hi,
This is because IGV filters out some reads when it displays them, such as bad quality, etc., you turn off all these filters and maybe you'll see the reads you want to see, hope that helps.
Shu Hu

[cpwater]

Hi, This is because IGV filters out some reads when it displays them, such as bad quality, etc., you turn off all these filters and maybe you'll see the reads you want to see, hope that helps. Shu Hu

Thanks so much! I'll try it!