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Old 04-09-2016, 11:27 AM   #1
TristanB
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Location: Tuebingen, DE

Join Date: May 2014
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Default Compare avg fragment length of major/minor allele reads at heterozygous position

Hi all,

I would like to compare average fragment length among reads contributing to a minor allele at a given heterozygous position vs average fragment length among reads contributing to the major allele at the same position. The reason I want to do this is quite complicated.

To my knowledge there is no straightforward way of doing this using SAMtools, and it would require a level of programming skill I do not have to try and coax such information out of a BAM file.

Is there some solution to this that I'm unaware of? So far the answer I've heard is 'no'.

I am entirely new here and this is my first post. In fact I'm generally new to bioinformatics and my training is in osteology and history.. odd the turns life can take. I'm not sure where this should go so if someone could kindly suggest the most appropriate discussion thread, that would be appreciated.
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