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Old 02-13-2020, 10:28 AM   #1
lorenzo.C
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Default find variants compared to sequenced reference

hi folks, I have 5 illumina sequencing fastq files. 1 is the parent and 4 are mutants. I alligned the sequence to the refenrence genome I have all the BAM bed etc etc files. I cleaned repetitive seq in the bam file with picard. what I would like to find are the variants (SNv and indels) that are present in each of the mutant strain but not in the parent. also I would like to have the variants just in the coding sequences. what program can I use?
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Old 02-13-2020, 11:38 AM   #2
GenoMax
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You need just step 1 from this tutorial since you only want SNv.
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Old 02-13-2020, 01:16 PM   #3
lorenzo.C
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isnt this command comparing a bam file to the reference genome? what I want are the SNV/indels present in the mutant strain but not in the control strain.
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Old 02-14-2020, 03:38 AM   #4
GenoMax
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You are identifying changes w.r.t. a reference and then comparing those results to get the difference between your control and mutant results.
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