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Old 12-11-2012, 12:09 AM   #2
pallevillesen
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Location: Bioinformatics Research Center, Aarhus University, Denmark

Join Date: May 2012
Posts: 19
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1) ? Reference has nothing - so it's a C insertion (?) I have never seen this in the documentation or in output... Can't help - sorry.

2) YES! That looks extremely suspicious. Check the raw alignment of the reads in IGV or similar

3) Probably mapping errors due to repeat seq or similar - remove them - You should make a histogram of the mapping depth and see if anything looks weird - but mapping errors (with mismatches) causes "SNPs/indels" to arise - and you don't want them.

My main suggestion: look at the raw data for these positions.
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