Finding SNV showing allele specific bias
I have a fastq.gz file. I want to know the SNV's in this file showing an allele specific bias ( Bias as SNV allele frequency >0.7) .How can I do that?
• 1,724 views
•
link
written
by
ishmahe16 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to find variant frequency of nonsynonymous mutations using R?
written by ashaji •
-
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
written by jeni •
-
adding allele frequencies to a vcf
written by erl1977 •
-
Calculating minor allele frequency for GnomAD VCF file
written by Jamie Watson •
-
Quicker way to know if a SNV is involved in a mismatch alignment
written by MarVi •
-
how to get low depth variants in vcf file (hetrozygous condition)
written by hafiz.talhamalik
-
Are my methods correct?
written by ishmahe16 •
-
Will random hexamer priming introduce SNP / SNV detection bias?
written by CY
-
tools to calculate Exac population specific frequency
written by jan
-
correct notation of indels/duplication in .vcf file
written by User6891
You're going to have better luck getting useful answers if you a) show evidence that you've tried to research this problem yourself b) tell us what you've tried, and c) provide more details
So i had 6 files 3 control and 3 primed files and had to find the most differentially expressed gene. Usong Galaxy I did FastQc then trimmed the seauences. Once that was done I did RNA STAR to aloign them followed by htseq Count . Once I had the bam files I did deseq2 and got the genes that I am looking for.
For the SNV thing I tried converting the bam file to bcf using samtools and then to vcf file . Once I had my vcf file I had done grep -c AF1 but I am stuck at that point.