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Hello!
I am new in next generation sequencing. I did the snp/indel calling for a illumina data set with samtools. Now i have to filter the snp´s and indels. For filtering the snps i calculated the percentage of reads whicht showed mit the exchanged nucleotide an which showed me the referenz.
The problem is how can i filter the indels. I have only the number of reads which cover the position and reads which supported the different allels.
Does anyone of you has an idea how i can calculated a percentage out of the read numbers to filter the indels or should i use the snp quality for filtering.
At which snp quality i should make my cut off?
Thank you
I am new in next generation sequencing. I did the snp/indel calling for a illumina data set with samtools. Now i have to filter the snp´s and indels. For filtering the snps i calculated the percentage of reads whicht showed mit the exchanged nucleotide an which showed me the referenz.
The problem is how can i filter the indels. I have only the number of reads which cover the position and reads which supported the different allels.
Does anyone of you has an idea how i can calculated a percentage out of the read numbers to filter the indels or should i use the snp quality for filtering.
At which snp quality i should make my cut off?
Thank you