Hello. I am a 1st year grad student in genetics lab. I am new to bioinformatics.

computer: MS-Linux ubuntu-miniconda3

data: fish tissue gDNA NGS(MGISEQ,, 150 paried end read) picard bam, bai file

My goals are

1. Compare sample seq with NCBI reference seq and find deletion sites(over 50bp) and download the result file containg site positon and deletion sequence
2. There are 22 chromosome bam file. I want to get each chromosome fasta file. (not 150bp multiple fasta but one whole aligned fasata file)

Which sv tools can I use? GATK? freebayes? Mutect2? delly?

And can you recommend some tutorial site or video?

Thank you so much for your attention.