find variants compared to sequenced reference

lorenzo.C · 02-13-2020, 11:28 AM

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, 12:38 PM

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

lorenzo.C · 02-13-2020, 02:16 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, 04:38 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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02-13-2020, 11:28 AM	#1
lorenzo.C Junior Member Location: berkeley Join Date: Jan 2018 Posts: 6	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?

02-13-2020, 12:38 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	You need just step 1 from this tutorial since you only want SNv.

02-13-2020, 02:16 PM	#3
lorenzo.C Junior Member Location: berkeley Join Date: Jan 2018 Posts: 6	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.

02-14-2020, 04:38 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	You are identifying changes w.r.t. a reference and then comparing those results to get the difference between your control and mutant results.