Question: Problem with indels not appearing in FreeBayes output
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melora.mackey • 10 wrote:
Hello,
I have 6 datasets for 3 individuals (forward and reverse DNA seuqences) that I am trying to identify polymorphic sites in reference to the human genome. I have performed FastQC, Fastq Groomer, Map with Bowtie for Illumina, addorreplacereadgroups, mergeSAMfiles, and performed FreeBayes and performed VCFfilter for -f "QUAL > 40". I am not seeing any insertions or deletions when looking at the FreeBayes data or when filtering for insertions or deletions. Other filters seem to be working such as filtering for snps, mnps, complex, and such. Does anyone know why I cannot see any indels in my output? Thanks in advance!
HI Do you see indels if you use 'Choose parameter selection> level 1:Simple diploid calling'
If you are using 'Choose parameter selection level>5:Complete list of all options' are you sure that 'Set allelic scope?>Ignore indels alleles' is set to its default no ?
What version of freebayes are you using? Guy