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?
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.