Question: Problem with indels not appearing in FreeBayes output
gravatar for melora.mackey
22 months ago by
melora.mackey10 wrote:


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!

freebayes • 626 views
ADD COMMENTlink written 22 months ago by melora.mackey10

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

ADD REPLYlink modified 22 months ago • written 22 months ago by Guy Reeves1.0k
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