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Forum: Bioinformatics 09-24-2012, 07:22 AM
Replies: 2
Views: 1,143
Posted By lchang1101
Thank you for the reply. No, I dont think MQ=20...

Thank you for the reply. No, I dont think MQ=20 was the problem. Some of the called variants in my run had MQ as low as 16. Any other thoughts?
Forum: Bioinformatics 09-23-2012, 07:18 PM
Replies: 2
Views: 1,143
Posted By lchang1101
samtools mpileup did not call variant

I used samtools mpileup and bcftools to call variants in my RNA-Seq data. At one locus, I have 10 reads that are different from the ref sequence (DP4=32,21,5,5), but bcftools did not call this...
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