find variants compared to sequenced reference in coding sequences

Question

[nibhelim]

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?

[nibhelim]

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

Answer 1

[JC]

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