Question: find variants compared to sequenced reference in coding sequences
0
gravatar for nibhelim
9 months ago by
nibhelim0
United States
nibhelim0 wrote:

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?

variant calling • 166 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by nibhelim0

can you suggest me a variant call that gives just variants in the mutant sample that are not in the control sample?

ADD REPLYlink written 9 months ago by nibhelim0
0
gravatar for JC
9 months ago by
JC12k
Mexico
JC12k wrote:

After variant call with your prefered software, you can filter the VCFs with vcftools or load them in Gemini and do filtering.

ADD COMMENTlink written 9 months ago by JC12k
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