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Itay.zemach 05-29-2015 12:26 AM

mutations file
Hello all,

I just finished generating BAM file of resequenced tomato line from paired end (reads size 100bp).
and view it through IGV (aligned to reference genome). Do you familiar with any way to load all mutations that were found in the resequenced line to one file instead of looking for them in IGV?

Thanks in advance,


GenoMax 05-29-2015 02:20 AM

When you refer to "mutations file" I assume you are referring to SNP's? You can use samtools to call SNP (and INDEL's too). Here is a simple guide (skip to the "Basic Variant Calling" section):

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