I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very much.
What I want in the end
A FASTA file containing a single sequential sequence (chromosome 1-22..) of the human genome.
What I have
- 23gb of "clean_data" which are .fq.gz files.
- 21gb of "result_alignment" which is .bam+.bai
- "result_variation" indel.vcf.gz and snp.vcf.gz
What I tried
samtools fasta reads.bam > reads.fasta which results in many lines like so:
>V100005418L4C001R001322578/1 AAATAGCCCACAC... >V100005418L4C001R006084507/1 GCCATAAAGCCTA... ...
But these include many many duplicate lines and the reference genome from the human genome project GRCh38 is only 3GB in size, so I thought that this FASTA sequence needs to be properly "aligned" somehow?
Am I thinking correctly here?
I'm really confused with all of the terminology and don't know exactly what I need to look for. Could someone kindly put the process into simpler words for me?