Suggestion required on analysing data
Hi,
Example of the data format,
I am required to parse through data sequenced from a family to identify if there are any CNVs present in the offspring. The data is from complete genomics. The question is here how to compare the data from parent and offspring with the common factor being the chromosome and read start and end position. Insights into how to compare the files will be helpful.
Best ~M
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You can compare files by importing data tables in R,
read.table()orread.delim(), and exploiting merge function and passing as parametersby=c("Chromosome","Start","End")andall=TRUE.My data is big for R and I get "negative length vectors are not allowed" error when I tried merging them. But thanks for the suggestion Nicola.
You tagged your post with "CNV" and seem to have (questionable) data for that, but then you ask about InDels. The example dataset you posted doesn't seem to contain any information pertaining to InDels, so what do you actually want to do?
Sorry for that Devon, I have now uploaded a link to full file format. I want to compare the calledploidy for parents and offspring within specific interval. The window size is same for both the parents and offspring. Based on the value of calledPloidy, I have to filter out the ones above a specific threshold score and annotate them with reference and compare for known CNV in databases.
A simple little (~20 lines) python or perl program would suffice for all of that.
man commandman diff