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How to find variant frequency of nonsynonymous mutations using R?
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SNV occuring 2 fold more in forward than in reverse reads should be filtered?
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adding allele frequencies to a vcf
written by erl1977 6Hi all, I have a vcf file generated from a few hundred samples. For each variant within the file, I would like to calculate the …
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Calculating minor allele frequency for GnomAD VCF file
written by Jamie Watson 2I have downloaded GnomAD vcf file and want to calculate the minor allele frequency of each variant in that file. But I am not quite …
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Quicker way to know if a SNV is involved in a mismatch alignment
written by MarVi 3Dear all, I have an advice to ask. I have a collection of alignments, of which I want to know if the mismatches found in …
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how to get low depth variants in vcf file (hetrozygous condition)
written by hafiz.talhamalik 35I want to get a variant in vcf file which is present in hetrozygous condition. for example if at a specific position 50 reads get …
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Are my methods correct?
written by ishmahe16 0File name Description Tcas5.2.fna.gz Tribolium castaneum reference genome (build 5.2) in fasta format. (X-chromosome and Autosomes only) Tcas5.2.gff.gz Corresponding GFF file for the Tcas5.2 reference …
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Will random hexamer priming introduce SNP / SNV detection bias?
written by CY 77Certain hexamer primers are favored during PCR step and this will cause allele frequency bias in the alignment. I image this bias will affect SNP …
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tools to calculate Exac population specific frequency
written by jan 19HI, I have 500+ MAF files of exome sequencing. I want to get the allele frequency for all population in Exac. I have used awk …
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correct notation of indels/duplication in .vcf file
written by User6891 34Hi everyone, I have to create an artificial .vcf file with SNVs, but also with small insertions, deletions and duplications, that will be used by …
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.