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lorenzo.C 02-13-2020 10:28 AM

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?

GenoMax 02-13-2020 11:38 AM

You need just step 1 from this tutorial since you only want SNv.

lorenzo.C 02-13-2020 01:16 PM

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.

GenoMax 02-14-2020 03:38 AM

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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